ERROR [2016-12-05 12:40:55,934] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,934] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,934] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,935] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,935] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,935] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,935] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,935] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,936] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,937] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,938] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,938] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,938] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,938] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,939] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,939] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,940] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,940] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,940] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,940] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,941] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,941] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,941] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,941] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,941] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,942] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,943] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,943] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,943] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,943] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,943] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,944] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
ERROR [2016-12-05 12:40:55,945] [ImportRegionsMenuAction.java:117]  Error importing regions of interest
java.lang.NumberFormatException: For input string: "0.000000e+00"
	at java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at java.lang.Integer.parseInt(Unknown Source)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.readRegionsOfInterestFile(ImportRegionsMenuAction.java:112)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.access$000(ImportRegionsMenuAction.java:48)
	at org.broad.igv.ui.action.ImportRegionsMenuAction$1.run(ImportRegionsMenuAction.java:67)
	at org.broad.igv.ui.util.UIUtilities.invokeOnEventThread(UIUtilities.java:150)
	at org.broad.igv.ui.action.ImportRegionsMenuAction.actionPerformed(ImportRegionsMenuAction.java:62)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.AbstractButton.doClick(Unknown Source)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
INFO [2016-12-05 13:08:59,158] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:08:59,159] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.txt
INFO [2016-12-05 13:09:59,412] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:09:59,412] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.txt
INFO [2016-12-05 13:10:02,112] [MessageUtils.java:74]  <html>Unknown file type: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.txt<br>Check file extension
INFO [2016-12-05 13:11:46,395] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:11:46,395] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.bed
INFO [2016-12-05 13:13:03,940] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2016-12-05 13:29:59,480] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:29:59,481] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak
ERROR [2016-12-05 13:29:59,485] [TrackLoader.java:256]  Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@64704e61, for input source: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak
htsjdk.tribble.TribbleException$MalformedFeatureFile: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@64704e61, for input source: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:355)
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.<init>(TribbleIndexedFeatureReader.java:309)
	at htsjdk.tribble.TribbleIndexedFeatureReader.iterator(TribbleIndexedFeatureReader.java:276)
	at org.broad.igv.feature.tribble.TribbleReaderWrapper.iterator(TribbleReaderWrapper.java:82)
	at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.<init>(TribbleFeatureSource.java:304)
	at org.broad.igv.track.TribbleFeatureSource$NonIndexedFeatureSource.<init>(TribbleFeatureSource.java:287)
	at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:96)
	at org.broad.igv.track.TribbleFeatureSource.getFeatureSource(TribbleFeatureSource.java:69)
	at org.broad.igv.track.TrackLoader.loadTribbleFile(TrackLoader.java:392)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:217)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NumberFormatException: For input string: "."
	at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
	at sun.misc.FloatingDecimal.parseFloat(Unknown Source)
	at java.lang.Float.parseFloat(Unknown Source)
	at org.broad.igv.feature.tribble.EncodePeakCodec.decode(EncodePeakCodec.java:95)
	at org.broad.igv.feature.tribble.EncodePeakCodec.decode(EncodePeakCodec.java:52)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
	at htsjdk.tribble.TribbleIndexedFeatureReader$WFIterator.readNextRecord(TribbleIndexedFeatureReader.java:341)
	... 18 more
ERROR [2016-12-05 13:29:59,486] [IGV.java:1725]  Error loading track
org.broad.igv.exceptions.DataLoadException: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@64704e61, for input source: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 13:29:59,486] [MessageUtils.java:74]  Error loading C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak: Error parsing line at byte position: htsjdk.tribble.readers.LineIteratorImpl@64704e61, for input source: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.broadPeak
INFO [2016-12-05 13:43:57,223] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:43:57,223] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1_1.igv
INFO [2016-12-05 13:45:36,007] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.igv.txt
INFO [2016-12-05 13:45:36,008] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 13:45:36,008] [IgvTools.java:676]  Window functions: mean percentile10 
INFO [2016-12-05 13:45:36,031] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-05 13:45:40,018] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 13:45:52,510] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 13:45:52,510] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.igv.txt.tdf
INFO [2016-12-05 19:00:17,133] [IgvTools.java:831]  Computing coverage.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaks1.igv
INFO [2016-12-05 19:00:17,134] [IgvTools.java:832]  Max zoom = 7
INFO [2016-12-05 19:00:17,134] [IgvTools.java:833]  Window size = 25
INFO [2016-12-05 19:00:17,134] [IgvTools.java:838]  Window functions: mean 
INFO [2016-12-05 19:00:17,134] [IgvTools.java:839]  Ext factor = 0
WARN [2016-12-05 19:00:17,190] [Preprocessor.java:328]  No features were found that matched chromosomes in genome: hg38
INFO [2016-12-05 19:02:47,793] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaks1.igv
INFO [2016-12-05 19:02:47,793] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:02:47,794] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:02:47,795] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-05 19:02:47,798] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 19:02:47,801] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:04:51,949] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaks1.igv
INFO [2016-12-05 19:04:51,949] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:04:51,949] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:04:51,950] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-05 19:04:51,953] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 19:04:51,956] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:05:07,691] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 19:05:07,691] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaks1.igv.tdf
INFO [2016-12-05 19:26:57,625] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaksplz.igv.txt
INFO [2016-12-05 19:26:57,625] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:26:57,626] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:26:57,627] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-05 19:26:57,628] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 19:26:57,630] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:27:23,508] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaksplz.igv.txt
INFO [2016-12-05 19:27:23,508] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:27:23,508] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:27:23,510] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-05 19:27:23,511] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 19:27:23,513] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:28:23,998] [ShutdownThread.java:51]  Shutting down
INFO [2016-12-05 19:28:34,059] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2016-12-05 19:28:34,060] [Main.java:134]  Java 1.8.0_111
INFO [2016-12-05 19:28:34,060] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2016-12-05 19:28:34,060] [Main.java:136]  OS: Windows 10
INFO [2016-12-05 19:28:35,220] [Main.java:184]  A later version of IGV is available (2.3.84)
INFO [2016-12-05 19:28:45,758] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2016-12-05 19:28:46,978] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2016-12-05 19:28:46,978] [Main.java:134]  Java 1.8.0_111
INFO [2016-12-05 19:28:46,978] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2016-12-05 19:28:46,979] [Main.java:136]  OS: Windows 10
INFO [2016-12-05 19:28:47,435] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2016-12-05 19:28:47,578] [CommandListener.java:106]  Listening on port 60151
INFO [2016-12-05 19:28:47,829] [Main.java:184]  A later version of IGV is available (2.3.84)
INFO [2016-12-05 19:28:58,092] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2016-12-05 19:28:59,653] [GenomeManager.java:192]  Genome loaded.  id= hg38
ERROR [2016-12-05 19:28:59,794] [CommandListener.java:124]  java.net.BindException: Address already in use: JVM_Bind
INFO [2016-12-05 19:29:02,161] [ShutdownThread.java:51]  Shutting down
INFO [2016-12-05 19:29:46,965] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaksplz.igv.txt
INFO [2016-12-05 19:29:46,965] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:29:46,966] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:29:46,976] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-05 19:29:46,984] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-05 19:29:47,021] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:30:33,081] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.igv.txt
INFO [2016-12-05 19:30:33,081] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-05 19:30:33,081] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-05 19:30:33,083] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-05 19:30:43,937] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-05 19:30:53,823] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 19:30:53,825] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.2.igv.txt.tdf
INFO [2016-12-05 19:32:23,207] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 19:32:23,207] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.2.igv.txt.tdf
INFO [2016-12-05 19:32:43,319] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-05 19:32:43,320] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaksplz2.igv.txt.tdf
INFO [2016-12-06 09:54:24,818] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_normPeaks1.igv
INFO [2016-12-06 09:54:24,820] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 09:54:24,820] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 09:54:24,822] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-06 09:54:24,824] [CNParser.java:215]  10
java.lang.ArrayIndexOutOfBoundsException: 10
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:196)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-06 09:54:24,826] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 10:09:46,719] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_extra.igv
INFO [2016-12-06 10:09:46,719] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 10:09:46,719] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 10:09:46,721] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-06 10:10:28,129] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 10:11:33,359] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks1.igv
INFO [2016-12-06 10:11:33,360] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 10:11:33,360] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 10:11:33,362] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-06 10:11:39,020] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 10:11:55,199] [ShutdownThread.java:51]  Shutting down
INFO [2016-12-06 10:12:03,616] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2016-12-06 10:12:03,616] [Main.java:134]  Java 1.8.0_111
INFO [2016-12-06 10:12:03,616] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2016-12-06 10:12:03,617] [Main.java:136]  OS: Windows 10
ERROR [2016-12-06 10:12:05,832] [Main.java:199]  Error checking version
java.net.SocketTimeoutException: Read timed out
	at java.net.SocketInputStream.socketRead0(Native Method)
	at java.net.SocketInputStream.socketRead(Unknown Source)
	at java.net.SocketInputStream.read(Unknown Source)
	at java.net.SocketInputStream.read(Unknown Source)
	at sun.security.ssl.InputRecord.readFully(Unknown Source)
	at sun.security.ssl.InputRecord.readV3Record(Unknown Source)
	at sun.security.ssl.InputRecord.read(Unknown Source)
	at sun.security.ssl.SSLSocketImpl.readRecord(Unknown Source)
	at sun.security.ssl.SSLSocketImpl.performInitialHandshake(Unknown Source)
	at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)
	at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)
	at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.HttpURLConnection.getResponseCode(Unknown Source)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(Unknown Source)
	at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:718)
	at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:735)
	at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:735)
	at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:623)
	at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:619)
	at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:143)
	at org.broad.igv.util.HttpUtils.getContentsAsString(HttpUtils.java:136)
	at org.broad.igv.ui.Main.checkVersion(Main.java:172)
	at org.broad.igv.ui.Main.initApplication(Main.java:147)
	at org.broad.igv.ui.Main.main(Main.java:87)
INFO [2016-12-06 10:12:16,178] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2016-12-06 10:12:17,517] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2016-12-06 10:12:17,648] [CommandListener.java:106]  Listening on port 60151
INFO [2016-12-06 10:12:23,807] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 10:12:23,809] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_extra.igv.tdf
INFO [2016-12-06 10:12:50,102] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 10:12:50,102] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks1.igv.tdf
INFO [2016-12-06 11:33:44,161] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 11:33:44,161] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\HypoxiaPeaks1.bed
INFO [2016-12-06 11:43:11,745] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2016-12-06 17:09:28,441] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\hyp_norm_chr1_tracks.igv
INFO [2016-12-06 17:09:28,442] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:09:28,442] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:09:28,449] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-06 17:09:34,491] [CNParser.java:215]  4
java.lang.ArrayIndexOutOfBoundsException: 4
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:198)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-06 17:09:34,582] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:11:37,335] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:11:37,335] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\hyp_norm_chr1_tracks.igv.tdf
INFO [2016-12-06 17:13:59,723] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\hyp_norm_chr1_tracks.igv
INFO [2016-12-06 17:13:59,723] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:13:59,723] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:13:59,739] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-06 17:14:05,865] [CNParser.java:215]  4
java.lang.ArrayIndexOutOfBoundsException: 4
	at org.broad.igv.tools.parsers.CNParser.parse(CNParser.java:198)
	at org.broad.igv.tools.Preprocessor.preprocess(Preprocessor.java:743)
	at org.broad.igv.tools.IgvTools.toTDF(IgvTools.java:726)
	at org.broad.igv.tools.IgvToolsGui$14.doInBackground(IgvToolsGui.java:508)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-06 17:14:05,961] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:22:58,379] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\hyp_norm_chr1_4tracks.igv
INFO [2016-12-06 17:22:58,379] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:22:58,379] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:22:58,379] [Preprocessor.java:255]  Processing chromosome chr1
ERROR [2016-12-06 17:23:04,514] [CNParser.java:215]  
java.lang.ArrayIndexOutOfBoundsException
INFO [2016-12-06 17:23:04,621] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:36:55,510] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:36:55,510] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt
INFO [2016-12-06 17:37:24,443] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt
INFO [2016-12-06 17:37:24,443] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:37:24,443] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:37:24,443] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-06 17:37:30,733] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:38:19,116] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:38:19,116] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf
INFO [2016-12-06 17:38:40,701] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt
INFO [2016-12-06 17:38:40,701] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:38:40,701] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:38:40,701] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-06 17:39:08,560] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:39:22,717] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:39:22,717] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf
INFO [2016-12-06 17:41:16,601] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_3.igv.txt
INFO [2016-12-06 17:41:16,601] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:41:16,601] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:41:16,603] [Preprocessor.java:255]  Processing chromosome chr1
WARN [2016-12-06 17:41:22,749] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659710  Locus = chr1:248956500-248956649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,749] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659711  Locus = chr1:248956650-248956799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,749] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659712  Locus = chr1:248956800-248956949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,749] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659713  Locus = chr1:248956950-248957099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659714  Locus = chr1:248957100-248957249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659715  Locus = chr1:248957250-248957399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659716  Locus = chr1:248957400-248957549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659717  Locus = chr1:248957550-248957699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659718  Locus = chr1:248957700-248957849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659719  Locus = chr1:248957850-248957999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,750] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659720  Locus = chr1:248958000-248958149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,751] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659721  Locus = chr1:248958150-248958299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,751] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659722  Locus = chr1:248958300-248958449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,751] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659723  Locus = chr1:248958450-248958599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,751] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659724  Locus = chr1:248958600-248958749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,751] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659725  Locus = chr1:248958750-248958899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659726  Locus = chr1:248958900-248959049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659727  Locus = chr1:248959050-248959199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659728  Locus = chr1:248959200-248959349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659729  Locus = chr1:248959350-248959499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659730  Locus = chr1:248959500-248959649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659731  Locus = chr1:248959650-248959799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659732  Locus = chr1:248959800-248959949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,752] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659733  Locus = chr1:248959950-248960099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659734  Locus = chr1:248960100-248960249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659735  Locus = chr1:248960250-248960399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659736  Locus = chr1:248960400-248960549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659737  Locus = chr1:248960550-248960699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659738  Locus = chr1:248960700-248960849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659739  Locus = chr1:248960850-248960999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659740  Locus = chr1:248961000-248961149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,753] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659741  Locus = chr1:248961150-248961299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,754] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659742  Locus = chr1:248961300-248961449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,754] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659743  Locus = chr1:248961450-248961599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,754] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659744  Locus = chr1:248961600-248961749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,754] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659745  Locus = chr1:248961750-248961899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,754] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659746  Locus = chr1:248961900-248962049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,755] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659747  Locus = chr1:248962050-248962199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,755] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659748  Locus = chr1:248962200-248962349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,755] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659749  Locus = chr1:248962350-248962499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,755] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659750  Locus = chr1:248962500-248962649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,755] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659751  Locus = chr1:248962650-248962799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659752  Locus = chr1:248962800-248962949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659753  Locus = chr1:248962950-248963099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659754  Locus = chr1:248963100-248963249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659755  Locus = chr1:248963250-248963399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659756  Locus = chr1:248963400-248963549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659757  Locus = chr1:248963550-248963699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659758  Locus = chr1:248963700-248963849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659759  Locus = chr1:248963850-248963999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659760  Locus = chr1:248964000-248964149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,756] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659761  Locus = chr1:248964150-248964299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659762  Locus = chr1:248964300-248964449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659763  Locus = chr1:248964450-248964599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659764  Locus = chr1:248964600-248964749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659765  Locus = chr1:248964750-248964899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659766  Locus = chr1:248964900-248965049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659767  Locus = chr1:248965050-248965199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,757] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659768  Locus = chr1:248965200-248965349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659769  Locus = chr1:248965350-248965499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659770  Locus = chr1:248965500-248965649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659771  Locus = chr1:248965650-248965799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659772  Locus = chr1:248965800-248965949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659773  Locus = chr1:248965950-248966099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659774  Locus = chr1:248966100-248966249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659775  Locus = chr1:248966250-248966399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659776  Locus = chr1:248966400-248966549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,758] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659777  Locus = chr1:248966550-248966699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659778  Locus = chr1:248966700-248966849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659779  Locus = chr1:248966850-248966999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659780  Locus = chr1:248967000-248967149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659781  Locus = chr1:248967150-248967299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659782  Locus = chr1:248967300-248967449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659783  Locus = chr1:248967450-248967599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659784  Locus = chr1:248967600-248967749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659785  Locus = chr1:248967750-248967899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,759] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659786  Locus = chr1:248967900-248968049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659787  Locus = chr1:248968050-248968199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659788  Locus = chr1:248968200-248968349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659789  Locus = chr1:248968350-248968499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659790  Locus = chr1:248968500-248968649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659791  Locus = chr1:248968650-248968799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659792  Locus = chr1:248968800-248968949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,760] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659793  Locus = chr1:248968950-248969099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659794  Locus = chr1:248969100-248969249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659795  Locus = chr1:248969250-248969399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659796  Locus = chr1:248969400-248969549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659797  Locus = chr1:248969550-248969699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659798  Locus = chr1:248969700-248969849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659799  Locus = chr1:248969850-248969999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659800  Locus = chr1:248970000-248970149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659801  Locus = chr1:248970150-248970299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659802  Locus = chr1:248970300-248970449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,761] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659803  Locus = chr1:248970450-248970599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659804  Locus = chr1:248970600-248970749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659805  Locus = chr1:248970750-248970899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659806  Locus = chr1:248970900-248971049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659807  Locus = chr1:248971050-248971199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659808  Locus = chr1:248971200-248971349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659809  Locus = chr1:248971350-248971499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659810  Locus = chr1:248971500-248971649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659811  Locus = chr1:248971650-248971799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659812  Locus = chr1:248971800-248971949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659813  Locus = chr1:248971950-248972099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,762] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659814  Locus = chr1:248972100-248972249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659815  Locus = chr1:248972250-248972399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659816  Locus = chr1:248972400-248972549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659817  Locus = chr1:248972550-248972699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659818  Locus = chr1:248972700-248972849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659819  Locus = chr1:248972850-248972999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659820  Locus = chr1:248973000-248973149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659821  Locus = chr1:248973150-248973299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659822  Locus = chr1:248973300-248973449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659823  Locus = chr1:248973450-248973599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659824  Locus = chr1:248973600-248973749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,763] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659825  Locus = chr1:248973750-248973899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659826  Locus = chr1:248973900-248974049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659827  Locus = chr1:248974050-248974199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659828  Locus = chr1:248974200-248974349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659829  Locus = chr1:248974350-248974499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659830  Locus = chr1:248974500-248974649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659831  Locus = chr1:248974650-248974799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659832  Locus = chr1:248974800-248974949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659833  Locus = chr1:248974950-248975099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659834  Locus = chr1:248975100-248975249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659835  Locus = chr1:248975250-248975399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,764] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659836  Locus = chr1:248975400-248975549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659837  Locus = chr1:248975550-248975699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659838  Locus = chr1:248975700-248975849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659839  Locus = chr1:248975850-248975999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659840  Locus = chr1:248976000-248976149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659841  Locus = chr1:248976150-248976299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659842  Locus = chr1:248976300-248976449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659843  Locus = chr1:248976450-248976599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659844  Locus = chr1:248976600-248976749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659845  Locus = chr1:248976750-248976899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659846  Locus = chr1:248976900-248977049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,765] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659847  Locus = chr1:248977050-248977199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659848  Locus = chr1:248977200-248977349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659849  Locus = chr1:248977350-248977499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659850  Locus = chr1:248977500-248977649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659851  Locus = chr1:248977650-248977799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659852  Locus = chr1:248977800-248977949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659853  Locus = chr1:248977950-248978099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659854  Locus = chr1:248978100-248978249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659855  Locus = chr1:248978250-248978399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659856  Locus = chr1:248978400-248978549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659857  Locus = chr1:248978550-248978699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,766] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659858  Locus = chr1:248978700-248978849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659859  Locus = chr1:248978850-248978999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659860  Locus = chr1:248979000-248979149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659861  Locus = chr1:248979150-248979299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659862  Locus = chr1:248979300-248979449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659863  Locus = chr1:248979450-248979599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659864  Locus = chr1:248979600-248979749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659865  Locus = chr1:248979750-248979899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659866  Locus = chr1:248979900-248980049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659867  Locus = chr1:248980050-248980199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,767] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659868  Locus = chr1:248980200-248980349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659869  Locus = chr1:248980350-248980499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659870  Locus = chr1:248980500-248980649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659871  Locus = chr1:248980650-248980799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659872  Locus = chr1:248980800-248980949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659873  Locus = chr1:248980950-248981099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659874  Locus = chr1:248981100-248981249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659875  Locus = chr1:248981250-248981399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659876  Locus = chr1:248981400-248981549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659877  Locus = chr1:248981550-248981699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659878  Locus = chr1:248981700-248981849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,768] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659879  Locus = chr1:248981850-248981999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659880  Locus = chr1:248982000-248982149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659881  Locus = chr1:248982150-248982299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659882  Locus = chr1:248982300-248982449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659883  Locus = chr1:248982450-248982599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659884  Locus = chr1:248982600-248982749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659885  Locus = chr1:248982750-248982899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659886  Locus = chr1:248982900-248983049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659887  Locus = chr1:248983050-248983199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659888  Locus = chr1:248983200-248983349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659889  Locus = chr1:248983350-248983499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,769] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659890  Locus = chr1:248983500-248983649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659891  Locus = chr1:248983650-248983799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659892  Locus = chr1:248983800-248983949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659893  Locus = chr1:248983950-248984099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659894  Locus = chr1:248984100-248984249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659895  Locus = chr1:248984250-248984399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659896  Locus = chr1:248984400-248984549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659897  Locus = chr1:248984550-248984699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659898  Locus = chr1:248984700-248984849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659899  Locus = chr1:248984850-248984999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659900  Locus = chr1:248985000-248985149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659901  Locus = chr1:248985150-248985299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659902  Locus = chr1:248985300-248985449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659903  Locus = chr1:248985450-248985599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659904  Locus = chr1:248985600-248985749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659905  Locus = chr1:248985750-248985899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659906  Locus = chr1:248985900-248986049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659907  Locus = chr1:248986050-248986199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659908  Locus = chr1:248986200-248986349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659909  Locus = chr1:248986350-248986499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659910  Locus = chr1:248986500-248986649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659911  Locus = chr1:248986650-248986799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659912  Locus = chr1:248986800-248986949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659913  Locus = chr1:248986950-248987099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659914  Locus = chr1:248987100-248987249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659915  Locus = chr1:248987250-248987399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659916  Locus = chr1:248987400-248987549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659917  Locus = chr1:248987550-248987699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659918  Locus = chr1:248987700-248987849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659919  Locus = chr1:248987850-248987999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659920  Locus = chr1:248988000-248988149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659921  Locus = chr1:248988150-248988299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659922  Locus = chr1:248988300-248988449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659923  Locus = chr1:248988450-248988599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659924  Locus = chr1:248988600-248988749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659925  Locus = chr1:248988750-248988899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659926  Locus = chr1:248988900-248989049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659927  Locus = chr1:248989050-248989199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659928  Locus = chr1:248989200-248989349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659929  Locus = chr1:248989350-248989499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659930  Locus = chr1:248989500-248989649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659931  Locus = chr1:248989650-248989799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659932  Locus = chr1:248989800-248989949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659933  Locus = chr1:248989950-248990099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659934  Locus = chr1:248990100-248990249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659935  Locus = chr1:248990250-248990399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659936  Locus = chr1:248990400-248990549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659937  Locus = chr1:248990550-248990699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659938  Locus = chr1:248990700-248990849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659939  Locus = chr1:248990850-248990999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659940  Locus = chr1:248991000-248991149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659941  Locus = chr1:248991150-248991299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659942  Locus = chr1:248991300-248991449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659943  Locus = chr1:248991450-248991599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659944  Locus = chr1:248991600-248991749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659945  Locus = chr1:248991750-248991899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659946  Locus = chr1:248991900-248992049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659947  Locus = chr1:248992050-248992199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659948  Locus = chr1:248992200-248992349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659949  Locus = chr1:248992350-248992499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659950  Locus = chr1:248992500-248992649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659951  Locus = chr1:248992650-248992799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659952  Locus = chr1:248992800-248992949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659953  Locus = chr1:248992950-248993099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659954  Locus = chr1:248993100-248993249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659955  Locus = chr1:248993250-248993399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659956  Locus = chr1:248993400-248993549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659957  Locus = chr1:248993550-248993699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659958  Locus = chr1:248993700-248993849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659959  Locus = chr1:248993850-248993999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659960  Locus = chr1:248994000-248994149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659961  Locus = chr1:248994150-248994299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659962  Locus = chr1:248994300-248994449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659963  Locus = chr1:248994450-248994599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659964  Locus = chr1:248994600-248994749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659965  Locus = chr1:248994750-248994899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659966  Locus = chr1:248994900-248995049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659967  Locus = chr1:248995050-248995199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659968  Locus = chr1:248995200-248995349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659969  Locus = chr1:248995350-248995499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659970  Locus = chr1:248995500-248995649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659971  Locus = chr1:248995650-248995799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659972  Locus = chr1:248995800-248995949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659973  Locus = chr1:248995950-248996099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659974  Locus = chr1:248996100-248996249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659975  Locus = chr1:248996250-248996399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659976  Locus = chr1:248996400-248996549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659977  Locus = chr1:248996550-248996699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659978  Locus = chr1:248996700-248996849. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659979  Locus = chr1:248996850-248996999. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659980  Locus = chr1:248997000-248997149. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659981  Locus = chr1:248997150-248997299. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659982  Locus = chr1:248997300-248997449. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659983  Locus = chr1:248997450-248997599. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659984  Locus = chr1:248997600-248997749. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659985  Locus = chr1:248997750-248997899. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659986  Locus = chr1:248997900-248998049. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659987  Locus = chr1:248998050-248998199. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659988  Locus = chr1:248998200-248998349. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659989  Locus = chr1:248998350-248998499. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659990  Locus = chr1:248998500-248998649. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659991  Locus = chr1:248998650-248998799. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659992  Locus = chr1:248998800-248998949. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659993  Locus = chr1:248998950-248999099. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659994  Locus = chr1:248999100-248999249. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659995  Locus = chr1:248999250-248999399. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659996  Locus = chr1:248999400-248999549. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659997  Locus = chr1:248999550-248999699. chr1 length = 248956422
WARN [2016-12-06 17:41:22,770] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659998  Locus = chr1:248999700-248999849. chr1 length = 248956422
INFO [2016-12-06 17:41:22,869] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:42:18,855] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:42:18,855] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf
INFO [2016-12-06 17:48:06,350] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv
INFO [2016-12-06 17:48:06,350] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-06 17:48:06,350] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-06 17:48:06,350] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-06 17:48:09,413] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-06 17:48:21,551] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-06 17:48:21,551] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf
INFO [2016-12-08 12:16:29,889] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_1_3tracks.igv
INFO [2016-12-08 12:16:29,890] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:16:29,890] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:16:29,891] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-08 12:16:32,953] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:16:50,849] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv
INFO [2016-12-08 12:16:50,849] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:16:50,849] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:16:50,851] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-08 12:17:10,923] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:17:56,761] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv
INFO [2016-12-08 12:17:56,762] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:17:56,762] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:17:56,763] [Preprocessor.java:255]  Processing chromosome chr1
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659711  Locus = chr1:248956500-248956649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659712  Locus = chr1:248956650-248956799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659713  Locus = chr1:248956800-248956949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659714  Locus = chr1:248956950-248957099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659715  Locus = chr1:248957100-248957249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,854] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659716  Locus = chr1:248957250-248957399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659717  Locus = chr1:248957400-248957549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659718  Locus = chr1:248957550-248957699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659719  Locus = chr1:248957700-248957849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659720  Locus = chr1:248957850-248957999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659721  Locus = chr1:248958000-248958149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659722  Locus = chr1:248958150-248958299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659723  Locus = chr1:248958300-248958449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659724  Locus = chr1:248958450-248958599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659725  Locus = chr1:248958600-248958749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659726  Locus = chr1:248958750-248958899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659727  Locus = chr1:248958900-248959049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,855] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659728  Locus = chr1:248959050-248959199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659729  Locus = chr1:248959200-248959349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659730  Locus = chr1:248959350-248959499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659731  Locus = chr1:248959500-248959649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659732  Locus = chr1:248959650-248959799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659733  Locus = chr1:248959800-248959949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659734  Locus = chr1:248959950-248960099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659735  Locus = chr1:248960100-248960249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659736  Locus = chr1:248960250-248960399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659737  Locus = chr1:248960400-248960549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659738  Locus = chr1:248960550-248960699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,856] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659739  Locus = chr1:248960700-248960849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659740  Locus = chr1:248960850-248960999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659741  Locus = chr1:248961000-248961149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659742  Locus = chr1:248961150-248961299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659743  Locus = chr1:248961300-248961449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659744  Locus = chr1:248961450-248961599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659745  Locus = chr1:248961600-248961749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659746  Locus = chr1:248961750-248961899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659747  Locus = chr1:248961900-248962049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659748  Locus = chr1:248962050-248962199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659749  Locus = chr1:248962200-248962349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659750  Locus = chr1:248962350-248962499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659751  Locus = chr1:248962500-248962649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,857] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659752  Locus = chr1:248962650-248962799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659753  Locus = chr1:248962800-248962949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659754  Locus = chr1:248962950-248963099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659755  Locus = chr1:248963100-248963249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659756  Locus = chr1:248963250-248963399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659757  Locus = chr1:248963400-248963549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659758  Locus = chr1:248963550-248963699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659759  Locus = chr1:248963700-248963849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659760  Locus = chr1:248963850-248963999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659761  Locus = chr1:248964000-248964149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659762  Locus = chr1:248964150-248964299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659763  Locus = chr1:248964300-248964449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659764  Locus = chr1:248964450-248964599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,858] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659765  Locus = chr1:248964600-248964749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659766  Locus = chr1:248964750-248964899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659767  Locus = chr1:248964900-248965049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659768  Locus = chr1:248965050-248965199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659769  Locus = chr1:248965200-248965349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659770  Locus = chr1:248965350-248965499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659771  Locus = chr1:248965500-248965649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659772  Locus = chr1:248965650-248965799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659773  Locus = chr1:248965800-248965949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659774  Locus = chr1:248965950-248966099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659775  Locus = chr1:248966100-248966249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659776  Locus = chr1:248966250-248966399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659777  Locus = chr1:248966400-248966549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,859] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659778  Locus = chr1:248966550-248966699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659779  Locus = chr1:248966700-248966849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659780  Locus = chr1:248966850-248966999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659781  Locus = chr1:248967000-248967149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659782  Locus = chr1:248967150-248967299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659783  Locus = chr1:248967300-248967449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659784  Locus = chr1:248967450-248967599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659785  Locus = chr1:248967600-248967749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659786  Locus = chr1:248967750-248967899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659787  Locus = chr1:248967900-248968049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659788  Locus = chr1:248968050-248968199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659789  Locus = chr1:248968200-248968349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659790  Locus = chr1:248968350-248968499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659791  Locus = chr1:248968500-248968649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659792  Locus = chr1:248968650-248968799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,860] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659793  Locus = chr1:248968800-248968949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659794  Locus = chr1:248968950-248969099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659795  Locus = chr1:248969100-248969249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659796  Locus = chr1:248969250-248969399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659797  Locus = chr1:248969400-248969549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659798  Locus = chr1:248969550-248969699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659799  Locus = chr1:248969700-248969849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659800  Locus = chr1:248969850-248969999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659801  Locus = chr1:248970000-248970149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659802  Locus = chr1:248970150-248970299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659803  Locus = chr1:248970300-248970449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659804  Locus = chr1:248970450-248970599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659805  Locus = chr1:248970600-248970749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659806  Locus = chr1:248970750-248970899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,861] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659807  Locus = chr1:248970900-248971049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659808  Locus = chr1:248971050-248971199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659809  Locus = chr1:248971200-248971349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659810  Locus = chr1:248971350-248971499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659811  Locus = chr1:248971500-248971649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659812  Locus = chr1:248971650-248971799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659813  Locus = chr1:248971800-248971949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659814  Locus = chr1:248971950-248972099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659815  Locus = chr1:248972100-248972249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659816  Locus = chr1:248972250-248972399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659817  Locus = chr1:248972400-248972549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659818  Locus = chr1:248972550-248972699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659819  Locus = chr1:248972700-248972849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659820  Locus = chr1:248972850-248972999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,862] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659821  Locus = chr1:248973000-248973149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659822  Locus = chr1:248973150-248973299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659823  Locus = chr1:248973300-248973449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659824  Locus = chr1:248973450-248973599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659825  Locus = chr1:248973600-248973749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659826  Locus = chr1:248973750-248973899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659827  Locus = chr1:248973900-248974049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659828  Locus = chr1:248974050-248974199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659829  Locus = chr1:248974200-248974349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659830  Locus = chr1:248974350-248974499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659831  Locus = chr1:248974500-248974649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659832  Locus = chr1:248974650-248974799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659833  Locus = chr1:248974800-248974949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659834  Locus = chr1:248974950-248975099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,863] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659835  Locus = chr1:248975100-248975249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659836  Locus = chr1:248975250-248975399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659837  Locus = chr1:248975400-248975549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659838  Locus = chr1:248975550-248975699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659839  Locus = chr1:248975700-248975849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659840  Locus = chr1:248975850-248975999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659841  Locus = chr1:248976000-248976149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659842  Locus = chr1:248976150-248976299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659843  Locus = chr1:248976300-248976449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659844  Locus = chr1:248976450-248976599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659845  Locus = chr1:248976600-248976749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659846  Locus = chr1:248976750-248976899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659847  Locus = chr1:248976900-248977049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659848  Locus = chr1:248977050-248977199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659849  Locus = chr1:248977200-248977349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,864] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659850  Locus = chr1:248977350-248977499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659851  Locus = chr1:248977500-248977649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659852  Locus = chr1:248977650-248977799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659853  Locus = chr1:248977800-248977949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659854  Locus = chr1:248977950-248978099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659855  Locus = chr1:248978100-248978249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659856  Locus = chr1:248978250-248978399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659857  Locus = chr1:248978400-248978549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659858  Locus = chr1:248978550-248978699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659859  Locus = chr1:248978700-248978849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659860  Locus = chr1:248978850-248978999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659861  Locus = chr1:248979000-248979149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659862  Locus = chr1:248979150-248979299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659863  Locus = chr1:248979300-248979449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,865] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659864  Locus = chr1:248979450-248979599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659865  Locus = chr1:248979600-248979749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659866  Locus = chr1:248979750-248979899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659867  Locus = chr1:248979900-248980049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659868  Locus = chr1:248980050-248980199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659869  Locus = chr1:248980200-248980349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659870  Locus = chr1:248980350-248980499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659871  Locus = chr1:248980500-248980649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659872  Locus = chr1:248980650-248980799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659873  Locus = chr1:248980800-248980949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659874  Locus = chr1:248980950-248981099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659875  Locus = chr1:248981100-248981249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659876  Locus = chr1:248981250-248981399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659877  Locus = chr1:248981400-248981549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,866] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659878  Locus = chr1:248981550-248981699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659879  Locus = chr1:248981700-248981849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659880  Locus = chr1:248981850-248981999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659881  Locus = chr1:248982000-248982149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659882  Locus = chr1:248982150-248982299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659883  Locus = chr1:248982300-248982449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659884  Locus = chr1:248982450-248982599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659885  Locus = chr1:248982600-248982749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659886  Locus = chr1:248982750-248982899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659887  Locus = chr1:248982900-248983049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659888  Locus = chr1:248983050-248983199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659889  Locus = chr1:248983200-248983349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659890  Locus = chr1:248983350-248983499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,867] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659891  Locus = chr1:248983500-248983649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659892  Locus = chr1:248983650-248983799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659893  Locus = chr1:248983800-248983949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659894  Locus = chr1:248983950-248984099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659895  Locus = chr1:248984100-248984249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659896  Locus = chr1:248984250-248984399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659897  Locus = chr1:248984400-248984549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659898  Locus = chr1:248984550-248984699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659899  Locus = chr1:248984700-248984849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659900  Locus = chr1:248984850-248984999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659901  Locus = chr1:248985000-248985149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,868] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659902  Locus = chr1:248985150-248985299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659903  Locus = chr1:248985300-248985449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659904  Locus = chr1:248985450-248985599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659905  Locus = chr1:248985600-248985749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659906  Locus = chr1:248985750-248985899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659907  Locus = chr1:248985900-248986049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659908  Locus = chr1:248986050-248986199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659909  Locus = chr1:248986200-248986349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659910  Locus = chr1:248986350-248986499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659911  Locus = chr1:248986500-248986649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659912  Locus = chr1:248986650-248986799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659913  Locus = chr1:248986800-248986949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659914  Locus = chr1:248986950-248987099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659915  Locus = chr1:248987100-248987249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,869] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659916  Locus = chr1:248987250-248987399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659917  Locus = chr1:248987400-248987549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659918  Locus = chr1:248987550-248987699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659919  Locus = chr1:248987700-248987849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659920  Locus = chr1:248987850-248987999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659921  Locus = chr1:248988000-248988149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659922  Locus = chr1:248988150-248988299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659923  Locus = chr1:248988300-248988449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659924  Locus = chr1:248988450-248988599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659925  Locus = chr1:248988600-248988749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659926  Locus = chr1:248988750-248988899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659927  Locus = chr1:248988900-248989049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659928  Locus = chr1:248989050-248989199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,870] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659929  Locus = chr1:248989200-248989349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659930  Locus = chr1:248989350-248989499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659931  Locus = chr1:248989500-248989649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659932  Locus = chr1:248989650-248989799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659933  Locus = chr1:248989800-248989949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659934  Locus = chr1:248989950-248990099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659935  Locus = chr1:248990100-248990249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659936  Locus = chr1:248990250-248990399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659937  Locus = chr1:248990400-248990549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659938  Locus = chr1:248990550-248990699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659939  Locus = chr1:248990700-248990849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659940  Locus = chr1:248990850-248990999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659941  Locus = chr1:248991000-248991149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659942  Locus = chr1:248991150-248991299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659943  Locus = chr1:248991300-248991449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,871] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659944  Locus = chr1:248991450-248991599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659945  Locus = chr1:248991600-248991749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659946  Locus = chr1:248991750-248991899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659947  Locus = chr1:248991900-248992049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659948  Locus = chr1:248992050-248992199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659949  Locus = chr1:248992200-248992349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659950  Locus = chr1:248992350-248992499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659951  Locus = chr1:248992500-248992649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659952  Locus = chr1:248992650-248992799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659953  Locus = chr1:248992800-248992949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659954  Locus = chr1:248992950-248993099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659955  Locus = chr1:248993100-248993249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659956  Locus = chr1:248993250-248993399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659957  Locus = chr1:248993400-248993549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,872] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659958  Locus = chr1:248993550-248993699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659959  Locus = chr1:248993700-248993849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659960  Locus = chr1:248993850-248993999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659961  Locus = chr1:248994000-248994149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659962  Locus = chr1:248994150-248994299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659963  Locus = chr1:248994300-248994449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659964  Locus = chr1:248994450-248994599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659965  Locus = chr1:248994600-248994749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659966  Locus = chr1:248994750-248994899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659967  Locus = chr1:248994900-248995049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659968  Locus = chr1:248995050-248995199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659969  Locus = chr1:248995200-248995349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659970  Locus = chr1:248995350-248995499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659971  Locus = chr1:248995500-248995649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,873] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659972  Locus = chr1:248995650-248995799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659973  Locus = chr1:248995800-248995949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659974  Locus = chr1:248995950-248996099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659975  Locus = chr1:248996100-248996249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659976  Locus = chr1:248996250-248996399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659977  Locus = chr1:248996400-248996549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659978  Locus = chr1:248996550-248996699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659979  Locus = chr1:248996700-248996849. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659980  Locus = chr1:248996850-248996999. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659981  Locus = chr1:248997000-248997149. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659982  Locus = chr1:248997150-248997299. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659983  Locus = chr1:248997300-248997449. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659984  Locus = chr1:248997450-248997599. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659985  Locus = chr1:248997600-248997749. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659986  Locus = chr1:248997750-248997899. chr1 length = 248956422
WARN [2016-12-08 12:18:00,874] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659987  Locus = chr1:248997900-248998049. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659988  Locus = chr1:248998050-248998199. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659989  Locus = chr1:248998200-248998349. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659990  Locus = chr1:248998350-248998499. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659991  Locus = chr1:248998500-248998649. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659992  Locus = chr1:248998650-248998799. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659993  Locus = chr1:248998800-248998949. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659994  Locus = chr1:248998950-248999099. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659995  Locus = chr1:248999100-248999249. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659996  Locus = chr1:248999250-248999399. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659997  Locus = chr1:248999400-248999549. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659998  Locus = chr1:248999550-248999699. chr1 length = 248956422
WARN [2016-12-08 12:18:00,875] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659999  Locus = chr1:248999700-248999849. chr1 length = 248956422
INFO [2016-12-08 12:18:00,894] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:19:35,390] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-08 12:19:35,391] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf
INFO [2016-12-08 12:22:59,795] [IGV.java:1700]  Loading 1 resources.
INFO [2016-12-08 12:22:59,796] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf
INFO [2016-12-08 12:46:21,950] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1.igv.txt
INFO [2016-12-08 12:46:21,950] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:46:21,950] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:46:21,950] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-08 12:46:35,972] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:49:39,482] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_2.igv.txt
INFO [2016-12-08 12:49:39,482] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:49:39,482] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:49:39,482] [Preprocessor.java:255]  Processing chromosome chr1
INFO [2016-12-08 12:50:01,322] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:51:00,692] [IgvTools.java:667]  toTDF.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_3.igv.txt
INFO [2016-12-08 12:51:00,693] [IgvTools.java:668]  Max zoom = 7
INFO [2016-12-08 12:51:00,693] [IgvTools.java:676]  Window functions: mean 
INFO [2016-12-08 12:51:00,694] [Preprocessor.java:255]  Processing chromosome chr1
WARN [2016-12-08 12:51:14,154] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659711  Locus = chr1:248956500-248956649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,154] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659712  Locus = chr1:248956650-248956799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659713  Locus = chr1:248956800-248956949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659714  Locus = chr1:248956950-248957099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659715  Locus = chr1:248957100-248957249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659716  Locus = chr1:248957250-248957399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659717  Locus = chr1:248957400-248957549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659718  Locus = chr1:248957550-248957699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659719  Locus = chr1:248957700-248957849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659720  Locus = chr1:248957850-248957999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659721  Locus = chr1:248958000-248958149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659722  Locus = chr1:248958150-248958299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659723  Locus = chr1:248958300-248958449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,155] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659724  Locus = chr1:248958450-248958599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659725  Locus = chr1:248958600-248958749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659726  Locus = chr1:248958750-248958899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659727  Locus = chr1:248958900-248959049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659728  Locus = chr1:248959050-248959199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659729  Locus = chr1:248959200-248959349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659730  Locus = chr1:248959350-248959499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659731  Locus = chr1:248959500-248959649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659732  Locus = chr1:248959650-248959799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659733  Locus = chr1:248959800-248959949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659734  Locus = chr1:248959950-248960099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659735  Locus = chr1:248960100-248960249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659736  Locus = chr1:248960250-248960399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659737  Locus = chr1:248960400-248960549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659738  Locus = chr1:248960550-248960699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659739  Locus = chr1:248960700-248960849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,156] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659740  Locus = chr1:248960850-248960999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659741  Locus = chr1:248961000-248961149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659742  Locus = chr1:248961150-248961299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659743  Locus = chr1:248961300-248961449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659744  Locus = chr1:248961450-248961599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659745  Locus = chr1:248961600-248961749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659746  Locus = chr1:248961750-248961899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659747  Locus = chr1:248961900-248962049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659748  Locus = chr1:248962050-248962199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659749  Locus = chr1:248962200-248962349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659750  Locus = chr1:248962350-248962499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,157] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659751  Locus = chr1:248962500-248962649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659752  Locus = chr1:248962650-248962799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659753  Locus = chr1:248962800-248962949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659754  Locus = chr1:248962950-248963099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659755  Locus = chr1:248963100-248963249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659756  Locus = chr1:248963250-248963399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659757  Locus = chr1:248963400-248963549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659758  Locus = chr1:248963550-248963699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659759  Locus = chr1:248963700-248963849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,158] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659760  Locus = chr1:248963850-248963999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659761  Locus = chr1:248964000-248964149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659762  Locus = chr1:248964150-248964299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659763  Locus = chr1:248964300-248964449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659764  Locus = chr1:248964450-248964599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659765  Locus = chr1:248964600-248964749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659766  Locus = chr1:248964750-248964899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659767  Locus = chr1:248964900-248965049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659768  Locus = chr1:248965050-248965199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659769  Locus = chr1:248965200-248965349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659770  Locus = chr1:248965350-248965499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659771  Locus = chr1:248965500-248965649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659772  Locus = chr1:248965650-248965799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659773  Locus = chr1:248965800-248965949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659774  Locus = chr1:248965950-248966099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,159] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659775  Locus = chr1:248966100-248966249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659776  Locus = chr1:248966250-248966399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659777  Locus = chr1:248966400-248966549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659778  Locus = chr1:248966550-248966699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659779  Locus = chr1:248966700-248966849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659780  Locus = chr1:248966850-248966999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659781  Locus = chr1:248967000-248967149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659782  Locus = chr1:248967150-248967299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659783  Locus = chr1:248967300-248967449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659784  Locus = chr1:248967450-248967599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659785  Locus = chr1:248967600-248967749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659786  Locus = chr1:248967750-248967899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659787  Locus = chr1:248967900-248968049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659788  Locus = chr1:248968050-248968199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659789  Locus = chr1:248968200-248968349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,160] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659790  Locus = chr1:248968350-248968499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659791  Locus = chr1:248968500-248968649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659792  Locus = chr1:248968650-248968799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659793  Locus = chr1:248968800-248968949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659794  Locus = chr1:248968950-248969099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659795  Locus = chr1:248969100-248969249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659796  Locus = chr1:248969250-248969399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659797  Locus = chr1:248969400-248969549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659798  Locus = chr1:248969550-248969699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659799  Locus = chr1:248969700-248969849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659800  Locus = chr1:248969850-248969999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659801  Locus = chr1:248970000-248970149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659802  Locus = chr1:248970150-248970299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,161] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659803  Locus = chr1:248970300-248970449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659804  Locus = chr1:248970450-248970599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659805  Locus = chr1:248970600-248970749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659806  Locus = chr1:248970750-248970899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659807  Locus = chr1:248970900-248971049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659808  Locus = chr1:248971050-248971199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659809  Locus = chr1:248971200-248971349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659810  Locus = chr1:248971350-248971499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659811  Locus = chr1:248971500-248971649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659812  Locus = chr1:248971650-248971799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659813  Locus = chr1:248971800-248971949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659814  Locus = chr1:248971950-248972099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,162] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659815  Locus = chr1:248972100-248972249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659816  Locus = chr1:248972250-248972399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659817  Locus = chr1:248972400-248972549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659818  Locus = chr1:248972550-248972699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659819  Locus = chr1:248972700-248972849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659820  Locus = chr1:248972850-248972999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659821  Locus = chr1:248973000-248973149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659822  Locus = chr1:248973150-248973299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659823  Locus = chr1:248973300-248973449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659824  Locus = chr1:248973450-248973599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659825  Locus = chr1:248973600-248973749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659826  Locus = chr1:248973750-248973899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659827  Locus = chr1:248973900-248974049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659828  Locus = chr1:248974050-248974199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,163] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659829  Locus = chr1:248974200-248974349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659830  Locus = chr1:248974350-248974499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659831  Locus = chr1:248974500-248974649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659832  Locus = chr1:248974650-248974799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659833  Locus = chr1:248974800-248974949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659834  Locus = chr1:248974950-248975099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659835  Locus = chr1:248975100-248975249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659836  Locus = chr1:248975250-248975399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659837  Locus = chr1:248975400-248975549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659838  Locus = chr1:248975550-248975699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659839  Locus = chr1:248975700-248975849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659840  Locus = chr1:248975850-248975999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659841  Locus = chr1:248976000-248976149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659842  Locus = chr1:248976150-248976299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,164] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659843  Locus = chr1:248976300-248976449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659844  Locus = chr1:248976450-248976599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659845  Locus = chr1:248976600-248976749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659846  Locus = chr1:248976750-248976899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659847  Locus = chr1:248976900-248977049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659848  Locus = chr1:248977050-248977199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659849  Locus = chr1:248977200-248977349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659850  Locus = chr1:248977350-248977499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659851  Locus = chr1:248977500-248977649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659852  Locus = chr1:248977650-248977799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659853  Locus = chr1:248977800-248977949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659854  Locus = chr1:248977950-248978099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659855  Locus = chr1:248978100-248978249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659856  Locus = chr1:248978250-248978399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659857  Locus = chr1:248978400-248978549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,165] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659858  Locus = chr1:248978550-248978699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659859  Locus = chr1:248978700-248978849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659860  Locus = chr1:248978850-248978999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659861  Locus = chr1:248979000-248979149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659862  Locus = chr1:248979150-248979299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659863  Locus = chr1:248979300-248979449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659864  Locus = chr1:248979450-248979599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659865  Locus = chr1:248979600-248979749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659866  Locus = chr1:248979750-248979899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659867  Locus = chr1:248979900-248980049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659868  Locus = chr1:248980050-248980199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659869  Locus = chr1:248980200-248980349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659870  Locus = chr1:248980350-248980499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659871  Locus = chr1:248980500-248980649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659872  Locus = chr1:248980650-248980799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659873  Locus = chr1:248980800-248980949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,166] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659874  Locus = chr1:248980950-248981099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659875  Locus = chr1:248981100-248981249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659876  Locus = chr1:248981250-248981399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659877  Locus = chr1:248981400-248981549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659878  Locus = chr1:248981550-248981699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659879  Locus = chr1:248981700-248981849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659880  Locus = chr1:248981850-248981999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659881  Locus = chr1:248982000-248982149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659882  Locus = chr1:248982150-248982299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659883  Locus = chr1:248982300-248982449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659884  Locus = chr1:248982450-248982599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659885  Locus = chr1:248982600-248982749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659886  Locus = chr1:248982750-248982899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659887  Locus = chr1:248982900-248983049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659888  Locus = chr1:248983050-248983199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659889  Locus = chr1:248983200-248983349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,167] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659890  Locus = chr1:248983350-248983499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659891  Locus = chr1:248983500-248983649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659892  Locus = chr1:248983650-248983799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659893  Locus = chr1:248983800-248983949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659894  Locus = chr1:248983950-248984099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659895  Locus = chr1:248984100-248984249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659896  Locus = chr1:248984250-248984399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659897  Locus = chr1:248984400-248984549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659898  Locus = chr1:248984550-248984699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659899  Locus = chr1:248984700-248984849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659900  Locus = chr1:248984850-248984999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659901  Locus = chr1:248985000-248985149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659902  Locus = chr1:248985150-248985299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659903  Locus = chr1:248985300-248985449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659904  Locus = chr1:248985450-248985599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659905  Locus = chr1:248985600-248985749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,168] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659906  Locus = chr1:248985750-248985899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659907  Locus = chr1:248985900-248986049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659908  Locus = chr1:248986050-248986199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659909  Locus = chr1:248986200-248986349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659910  Locus = chr1:248986350-248986499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659911  Locus = chr1:248986500-248986649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659912  Locus = chr1:248986650-248986799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659913  Locus = chr1:248986800-248986949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659914  Locus = chr1:248986950-248987099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659915  Locus = chr1:248987100-248987249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659916  Locus = chr1:248987250-248987399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659917  Locus = chr1:248987400-248987549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659918  Locus = chr1:248987550-248987699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,169] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659919  Locus = chr1:248987700-248987849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659920  Locus = chr1:248987850-248987999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659921  Locus = chr1:248988000-248988149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659922  Locus = chr1:248988150-248988299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659923  Locus = chr1:248988300-248988449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659924  Locus = chr1:248988450-248988599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659925  Locus = chr1:248988600-248988749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659926  Locus = chr1:248988750-248988899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659927  Locus = chr1:248988900-248989049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659928  Locus = chr1:248989050-248989199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659929  Locus = chr1:248989200-248989349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659930  Locus = chr1:248989350-248989499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659931  Locus = chr1:248989500-248989649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659932  Locus = chr1:248989650-248989799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659933  Locus = chr1:248989800-248989949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,170] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659934  Locus = chr1:248989950-248990099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659935  Locus = chr1:248990100-248990249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659936  Locus = chr1:248990250-248990399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659937  Locus = chr1:248990400-248990549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659938  Locus = chr1:248990550-248990699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659939  Locus = chr1:248990700-248990849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659940  Locus = chr1:248990850-248990999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659941  Locus = chr1:248991000-248991149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659942  Locus = chr1:248991150-248991299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659943  Locus = chr1:248991300-248991449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659944  Locus = chr1:248991450-248991599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659945  Locus = chr1:248991600-248991749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659946  Locus = chr1:248991750-248991899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659947  Locus = chr1:248991900-248992049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659948  Locus = chr1:248992050-248992199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659949  Locus = chr1:248992200-248992349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,171] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659950  Locus = chr1:248992350-248992499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659951  Locus = chr1:248992500-248992649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659952  Locus = chr1:248992650-248992799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659953  Locus = chr1:248992800-248992949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659954  Locus = chr1:248992950-248993099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659955  Locus = chr1:248993100-248993249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659956  Locus = chr1:248993250-248993399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659957  Locus = chr1:248993400-248993549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659958  Locus = chr1:248993550-248993699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659959  Locus = chr1:248993700-248993849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659960  Locus = chr1:248993850-248993999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659961  Locus = chr1:248994000-248994149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659962  Locus = chr1:248994150-248994299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659963  Locus = chr1:248994300-248994449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659964  Locus = chr1:248994450-248994599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,172] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659965  Locus = chr1:248994600-248994749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659966  Locus = chr1:248994750-248994899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659967  Locus = chr1:248994900-248995049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659968  Locus = chr1:248995050-248995199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659969  Locus = chr1:248995200-248995349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659970  Locus = chr1:248995350-248995499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659971  Locus = chr1:248995500-248995649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659972  Locus = chr1:248995650-248995799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659973  Locus = chr1:248995800-248995949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659974  Locus = chr1:248995950-248996099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659975  Locus = chr1:248996100-248996249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659976  Locus = chr1:248996250-248996399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659977  Locus = chr1:248996400-248996549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659978  Locus = chr1:248996550-248996699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659979  Locus = chr1:248996700-248996849. chr1 length = 248956422
WARN [2016-12-08 12:51:14,173] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659980  Locus = chr1:248996850-248996999. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659981  Locus = chr1:248997000-248997149. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659982  Locus = chr1:248997150-248997299. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659983  Locus = chr1:248997300-248997449. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659984  Locus = chr1:248997450-248997599. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659985  Locus = chr1:248997600-248997749. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659986  Locus = chr1:248997750-248997899. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659987  Locus = chr1:248997900-248998049. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659988  Locus = chr1:248998050-248998199. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659989  Locus = chr1:248998200-248998349. chr1 length = 248956422
WARN [2016-12-08 12:51:14,174] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659990  Locus = chr1:248998350-248998499. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659991  Locus = chr1:248998500-248998649. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659992  Locus = chr1:248998650-248998799. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659993  Locus = chr1:248998800-248998949. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659994  Locus = chr1:248998950-248999099. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659995  Locus = chr1:248999100-248999249. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659996  Locus = chr1:248999250-248999399. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659997  Locus = chr1:248999400-248999549. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659998  Locus = chr1:248999550-248999699. chr1 length = 248956422
WARN [2016-12-08 12:51:14,175] [Preprocessor.java:199]  Ignoring data from non-existent locus.  Probe = 1659999  Locus = chr1:248999700-248999849. chr1 length = 248956422
INFO [2016-12-08 12:51:14,991] [TDFWriter.java:318]  Group idx: 1
INFO [2016-12-08 12:52:00,045] [IGV.java:1700]  Loading 6 resources.
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1f.igv.txt.tdf
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_2F.igv.txt.tdf
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_3F.igv.txt.tdf
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_1_3tracks.igv.tdf
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_2_3tracks.igv.tdf
INFO [2016-12-08 12:52:00,045] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_3_3tracks.igv.tdf
INFO [2016-12-09 12:38:48,835] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf_hypDensityhyp_Dens in session file
INFO [2016-12-09 12:38:48,864] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_normDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_normDensitynormDensity12C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf_normDensitynorm_Dens in session file
INFO [2016-12-09 12:38:48,865] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_hyp-normDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_hyp-normDensitySumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_hyp-normDensitySum in session file
INFO [2016-12-09 12:38:48,866] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_hyp-normRateC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_hyp-normRateSumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_hyp-normRateSum in session file
INFO [2016-12-09 12:38:48,867] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_HIF site/difference in chip densC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_HIF site/difference in chip densSumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_HIF site/difference in chip densSum in session file
ERROR [2016-12-09 12:38:48,868] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\hyp_norm_draft.xml<br>Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.data.CombinedDataSource.updateTrackReference(CombinedDataSource.java:100)
	at org.broad.igv.data.CombinedDataSource.updateTrackReferences(CombinedDataSource.java:92)
	at org.broad.igv.track.DataSourceTrack.updateTrackReferences(DataSourceTrack.java:185)
	at org.broad.igv.session.IGVSessionReader.processPanel(IGVSessionReader.java:1027)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:551)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1261)
	at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:472)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:325)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2016-12-09 12:38:48,869] [MessageUtils.java:74]  <html>Unexpected error: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum.<br>See igv.log for more details
ERROR [2016-12-09 12:39:01,666] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.data.CombinedDataSource.updateTrackReference(CombinedDataSource.java:100)
	at org.broad.igv.data.CombinedDataSource.updateTrackReferences(CombinedDataSource.java:92)
	at org.broad.igv.track.DataSourceTrack.updateTrackReferences(DataSourceTrack.java:185)
	at org.broad.igv.session.IGVSessionReader.processPanel(IGVSessionReader.java:1027)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:551)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1261)
	at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:472)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:325)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
INFO [2016-12-09 12:39:23,399] [IGV.java:1700]  Loading 6 resources.
INFO [2016-12-09 12:39:23,399] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1f.igv.txt.tdf
INFO [2016-12-09 12:39:23,399] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_2F.igv.txt.tdf
INFO [2016-12-09 12:39:23,399] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_3F.igv.txt.tdf
INFO [2016-12-09 12:39:23,415] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_1_3tracks.igv.tdf
INFO [2016-12-09 12:39:23,415] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_2_3tracks.igv.tdf
INFO [2016-12-09 12:39:23,415] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_3_3tracks.igv.tdf
INFO [2016-12-19 20:48:18,942] [ShutdownThread.java:51]  Shutting down
INFO [2017-05-30 13:45:52,678] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-05-30 13:45:52,685] [Main.java:134]  Java 1.8.0_101
INFO [2017-05-30 13:45:52,686] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-05-30 13:45:52,686] [Main.java:136]  OS: Windows 10
INFO [2017-05-30 13:45:54,796] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-05-30 13:46:04,759] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-05-30 13:46:04,759] [Main.java:134]  Java 1.8.0_111
INFO [2017-05-30 13:46:04,759] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-05-30 13:46:04,760] [Main.java:136]  OS: Windows 10
INFO [2017-05-30 13:46:06,410] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-05-30 13:46:07,081] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-05-30 13:46:08,909] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-05-30 13:46:09,143] [CommandListener.java:106]  Listening on port 60151
INFO [2017-05-30 13:46:19,851] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-05-30 13:46:21,286] [GenomeManager.java:192]  Genome loaded.  id= hg38
ERROR [2017-05-30 13:46:21,598] [CommandListener.java:124]  java.net.BindException: Address already in use: JVM_Bind
INFO [2017-05-30 13:46:31,702] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 13:46:31,704] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1.igv.txt
INFO [2017-05-30 13:48:17,943] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf_hypDensityhyp_Dens in session file
INFO [2017-05-30 13:48:18,065] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_normDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_normDensitynormDensity12C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf_normDensitynorm_Dens in session file
INFO [2017-05-30 13:48:18,066] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_hyp-normDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_hyp-normDensitySumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_hyp-normDensitySum in session file
INFO [2017-05-30 13:48:18,067] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_hyp-normRateC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_hyp-normRateSumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_hyp-normRateSum in session file
INFO [2017-05-30 13:48:18,068] [IGVSessionReader.java:1085]  Warning.  No tracks were found with id: C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_1_3tracks.igv.tdf_HIF site/difference in chip densC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_2_3tracks.igv.tdf_HIF site/difference in chip densSumC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\chr1_3_3tracks.igv.tdf_HIF site/difference in chip densSum in session file
ERROR [2017-05-30 13:48:18,070] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\hyp_norm_draft.xml<br>Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.data.CombinedDataSource.updateTrackReference(CombinedDataSource.java:100)
	at org.broad.igv.data.CombinedDataSource.updateTrackReferences(CombinedDataSource.java:92)
	at org.broad.igv.track.DataSourceTrack.updateTrackReferences(DataSourceTrack.java:185)
	at org.broad.igv.session.IGVSessionReader.processPanel(IGVSessionReader.java:1027)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:551)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1261)
	at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:472)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:325)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
INFO [2017-05-30 13:48:18,073] [MessageUtils.java:74]  <html>Unexpected error: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum.<br>See igv.log for more details
ERROR [2017-05-30 13:48:20,563] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: Could not find track with ID C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_1.igv.txt.tdf_hypDensityC:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks_chr1_2.igv.txt.tdf_hypDensitySum
	at org.broad.igv.data.CombinedDataSource.updateTrackReference(CombinedDataSource.java:100)
	at org.broad.igv.data.CombinedDataSource.updateTrackReferences(CombinedDataSource.java:92)
	at org.broad.igv.track.DataSourceTrack.updateTrackReferences(DataSourceTrack.java:185)
	at org.broad.igv.session.IGVSessionReader.processPanel(IGVSessionReader.java:1027)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:551)
	at org.broad.igv.session.IGVSessionReader.process(IGVSessionReader.java:1261)
	at org.broad.igv.session.IGVSessionReader.processRootNode(IGVSessionReader.java:472)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:325)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
ERROR [2017-05-30 13:48:33,249] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-05-30 13:48:33,250] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\Hypoxia_norm_densPeaks_chr1_3.igv.txt.tdf<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:48:33,252] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
ERROR [2017-05-30 13:48:35,498] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
ERROR [2017-05-30 13:48:49,388] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-05-30 13:48:49,388] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1.igv.txt<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:48:49,389] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
ERROR [2017-05-30 13:48:52,178] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
ERROR [2017-05-30 13:48:57,035] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
ERROR [2017-05-30 13:48:57,036] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1.igv.txt<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:48:57,036] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
ERROR [2017-05-30 13:49:02,610] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:49:03,575] [ShutdownThread.java:51]  Shutting down
INFO [2017-05-30 13:49:05,624] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-05-30 13:49:05,625] [Main.java:134]  Java 1.8.0_111
INFO [2017-05-30 13:49:05,625] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-05-30 13:49:05,626] [Main.java:136]  OS: Windows 10
INFO [2017-05-30 13:49:06,664] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-05-30 13:49:16,846] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
ERROR [2017-05-30 13:49:17,752] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 13:49:17,759] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_1.igv.txt<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:49:17,760] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
INFO [2017-05-30 13:49:18,565] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-05-30 13:49:18,702] [CommandListener.java:106]  Listening on port 60151
ERROR [2017-05-30 13:49:18,843] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
ERROR [2017-05-30 13:49:24,960] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 13:49:24,960] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\Hypoxia_norm_densPeaks_chr1_2.igv.txt<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:49:24,961] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
ERROR [2017-05-30 13:49:25,738] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
ERROR [2017-05-30 13:49:31,943] [IGVSessionReader.java:309]  Load session error
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 13:49:31,943] [IGV.java:1507]  Error loading session session : <br>&nbsp;&nbsp;C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\yes\yessir\chr1_1_3tracks.igv.tdf<br>org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:49:31,943] [MessageUtils.java:74]  <html>Unexpected error: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog..<br>See igv.log for more details
ERROR [2017-05-30 13:49:32,890] [LongRunningTask.java:75]  Exception running task
java.lang.RuntimeException: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1508)
	at org.broad.igv.ui.IGV$10.run(IGV.java:1442)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:310)
	at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1473)
	... 6 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(Unknown Source)
	at org.broad.igv.util.Utilities.createDOMDocumentFromXmlStream(Utilities.java:110)
	at org.broad.igv.session.IGVSessionReader.loadSession(IGVSessionReader.java:307)
	... 7 more
INFO [2017-05-30 13:49:56,126] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\Hypoxia_norm_densPeaks1.igv.tdf
INFO [2017-05-30 13:49:56,126] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\igv\chr1_extra.igv.tdf
INFO [2017-05-30 13:50:43,144] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 13:50:43,145] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-05-30 13:55:29,860] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-05-30 13:59:33,324] [ShutdownThread.java:51]  Shutting down
INFO [2017-05-30 14:05:52,476] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:05:52,476] [TrackLoader.java:120]  Loading resource, path https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/Homo_sapiens.GRCh38.80.sorted.gtf.gz
INFO [2017-05-30 14:06:45,348] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:06:45,349] [MessageUtils.java:74]  File not found: bigDataUrl=http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam

INFO [2017-05-30 14:07:02,756] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:07:02,756] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
ERROR [2017-05-30 14:07:02,844] [TrackLoader.java:256]  An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai
	at org.broad.igv.sam.reader.BAMHttpReader.getIndexStream(BAMHttpReader.java:204)
	at org.broad.igv.sam.reader.BAMHttpReader.getSamReader(BAMHttpReader.java:92)
	at org.broad.igv.sam.reader.BAMHttpReader.<init>(BAMHttpReader.java:73)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:94)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:63)
	at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:81)
	at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:915)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:174)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 14:07:02,844] [IGV.java:1725]  Error loading track
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2017-05-30 14:07:02,844] [MessageUtils.java:74]  Error loading http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bai
INFO [2017-05-30 14:08:33,283] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:08:33,284] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-05-30 14:08:33,325] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-05-30 14:18:55,210] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:18:55,211] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam
ERROR [2017-05-30 14:18:55,219] [TrackLoader.java:256]  An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai
	at org.broad.igv.sam.reader.BAMHttpReader.getIndexStream(BAMHttpReader.java:204)
	at org.broad.igv.sam.reader.BAMHttpReader.getSamReader(BAMHttpReader.java:92)
	at org.broad.igv.sam.reader.BAMHttpReader.<init>(BAMHttpReader.java:73)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:94)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:63)
	at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:81)
	at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:915)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:174)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 14:18:55,219] [IGV.java:1725]  Error loading track
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2017-05-30 14:18:55,220] [MessageUtils.java:74]  Error loading http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_VerySensitiveLocalSortedRmDup.bai
INFO [2017-05-30 14:19:54,410] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:19:54,410] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-05-30 14:25:37,653] [ShutdownThread.java:51]  Shutting down
INFO [2017-05-30 14:25:42,178] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-05-30 14:25:42,178] [Main.java:134]  Java 1.8.0_111
INFO [2017-05-30 14:25:42,178] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-05-30 14:25:42,179] [Main.java:136]  OS: Windows 10
INFO [2017-05-30 14:25:43,589] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-05-30 14:25:49,721] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-05-30 14:25:49,721] [Main.java:134]  Java 1.8.0_111
INFO [2017-05-30 14:25:49,721] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-05-30 14:25:49,721] [Main.java:136]  OS: Windows 10
INFO [2017-05-30 14:25:50,575] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-05-30 14:25:54,208] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-05-30 14:25:55,895] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-05-30 14:25:56,054] [CommandListener.java:106]  Listening on port 60151
INFO [2017-05-30 14:26:01,282] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-05-30 14:26:02,778] [GenomeManager.java:192]  Genome loaded.  id= hg38
ERROR [2017-05-30 14:26:02,912] [CommandListener.java:124]  java.net.BindException: Address already in use: JVM_Bind
INFO [2017-05-30 14:26:12,299] [ShutdownThread.java:51]  Shutting down
INFO [2017-05-30 14:26:19,820] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:26:19,821] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-05-30 14:26:19,847] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-05-30 14:26:42,930] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:26:42,931] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam
ERROR [2017-05-30 14:26:42,941] [TrackLoader.java:256]  An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai
	at org.broad.igv.sam.reader.BAMHttpReader.getIndexStream(BAMHttpReader.java:204)
	at org.broad.igv.sam.reader.BAMHttpReader.getSamReader(BAMHttpReader.java:92)
	at org.broad.igv.sam.reader.BAMHttpReader.<init>(BAMHttpReader.java:73)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:94)
	at org.broad.igv.sam.reader.AlignmentReaderFactory.getReader(AlignmentReaderFactory.java:63)
	at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:81)
	at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:915)
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:174)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
ERROR [2017-05-30 14:26:42,942] [IGV.java:1725]  Error loading track
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:258)
	at org.broad.igv.ui.IGV.load(IGV.java:1808)
	at org.broad.igv.ui.IGV$13.run(IGV.java:1721)
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1734)
	at org.broad.igv.ui.IGV$5.run(IGV.java:738)
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
INFO [2017-05-30 14:26:42,944] [MessageUtils.java:74]  Error loading http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam: An error occurred while accessing:    http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai<br>Index file not found.  Tried <br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bam.bai<br>http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalRmDup.bai
INFO [2017-05-30 14:26:59,753] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:26:59,753] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-05-30 14:27:06,084] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:27:06,085] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-05-30 14:27:25,212] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-30 14:27:25,212] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-05-30 14:27:52,923] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-05-31 12:25:07,223] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-31 12:25:07,223] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxiaReMadeVerySensitiveLocalSortedRmDup.bam
INFO [2017-05-31 12:26:38,758] [IGV.java:1700]  Loading 1 resources.
INFO [2017-05-31 12:26:38,758] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaReMadeverySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 09:31:59,239] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-06-01 09:31:59,238] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-06-01 09:31:59,301] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaReMadeverySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 09:31:59,339] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 09:31:59,758] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxiaReMadeVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 09:31:59,798] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-06-01 12:09:46,398] [IGV.java:1700]  Loading 15 resources.
INFO [2017-06-01 12:09:46,398] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/SINE.bed.gz
INFO [2017-06-01 12:09:46,951] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-01 12:09:49,179] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/LINE.bed.gz
INFO [2017-06-01 12:09:51,965] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/LTR.bed.gz
INFO [2017-06-01 12:09:54,464] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/DNA.bed.gz
INFO [2017-06-01 12:09:56,799] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/Simple_repeat.bed.gz
INFO [2017-06-01 12:09:59,260] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/Low_complexity.bed.gz
INFO [2017-06-01 12:10:01,537] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/Satellite.bed.gz
INFO [2017-06-01 12:10:02,516] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/RC.bed.gz
INFO [2017-06-01 12:10:03,025] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/Retroposon.bed.gz
INFO [2017-06-01 12:10:03,500] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/RNA.bed.gz
INFO [2017-06-01 12:10:03,916] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/rRNA.bed.gz
INFO [2017-06-01 12:10:04,329] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/scRNA.bed.gz
INFO [2017-06-01 12:10:04,769] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/snRNA.bed.gz
INFO [2017-06-01 12:10:05,222] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/srpRNA.bed.gz
INFO [2017-06-01 12:10:05,756] [TrackLoader.java:120]  Loading resource, path https://data.broadinstitute.org/igvdata/annotations/hg38/rmsk/tRNA.bed.gz
INFO [2017-06-01 13:14:30,174] [IgvTools.java:831]  Computing coverage.  File = C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\igv_session.xml
INFO [2017-06-01 13:14:30,175] [IgvTools.java:832]  Max zoom = 7
INFO [2017-06-01 13:14:30,175] [IgvTools.java:833]  Window size = 25
INFO [2017-06-01 13:14:30,175] [IgvTools.java:838]  Window functions: mean 
INFO [2017-06-01 13:14:30,175] [IgvTools.java:839]  Ext factor = 0
WARN [2017-06-01 13:14:30,197] [Preprocessor.java:328]  No features were found that matched chromosomes in genome: hg38
INFO [2017-06-01 17:36:13,078] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-01 17:36:37,170] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-06-01 17:36:37,170] [Main.java:134]  Java 1.8.0_101
INFO [2017-06-01 17:36:37,171] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-06-01 17:36:37,171] [Main.java:136]  OS: Windows 10
INFO [2017-06-01 17:36:38,802] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-06-01 17:36:48,649] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-01 17:36:50,123] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-01 17:36:50,253] [CommandListener.java:106]  Listening on port 60151
INFO [2017-06-01 17:37:02,818] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-06-01 17:37:02,818] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-06-01 17:37:02,950] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaReMadeverySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 17:37:02,994] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-01 17:37:03,149] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 17:37:03,174] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxiaReMadeVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-01 17:37:03,206] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-06-01 17:37:04,876] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-06 12:31:23,441] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-06-06 12:31:23,441] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-06-06 12:31:23,504] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaReMadeverySensitiveLocalSortedRmDup.bam
INFO [2017-06-06 12:31:23,817] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-06 12:31:23,858] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxiaReMadeVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-06 12:31:23,889] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-06-06 12:46:35,237] [GenomeManager.java:145]  Loading genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_016856.genome
INFO [2017-06-06 12:46:35,274] [URLDownloader.java:89]  Downloading http://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_016856.genome to C:\Users\Borchert\igv\genomes\NC_016856.genome
INFO [2017-06-06 12:46:36,464] [URLDownloader.java:130]  Download complete.  Total bytes downloaded = 2364522
INFO [2017-06-06 12:46:37,006] [GenomeManager.java:192]  Genome loaded.  id= NC_016856
INFO [2017-06-06 12:47:45,781] [IGV.java:1700]  Loading 1 resources.
INFO [2017-06-06 12:47:45,781] [TrackLoader.java:120]  Loading resource, path V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam
INFO [2017-06-06 12:47:45,797] [MessageUtils.java:74]  <html>File: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam<br>does not contain any sequence names which match the current genome.<br><br>File: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pRSF1010_SL1344, pCol1B9_SL1344, pSLT_SL1344, Chromosome,  ...<br>Genome: gi|378448274|ref|NC_016856.1|, 
INFO [2017-06-06 12:48:19,392] [IGV.java:1700]  Loading 1 resources.
INFO [2017-06-06 12:48:19,392] [TrackLoader.java:120]  Loading resource, path V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam
INFO [2017-06-06 12:48:19,392] [MessageUtils.java:74]  <html>File: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam<br>does not contain any sequence names which match the current genome.<br><br>File: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pRSF1010_SL1344, pCol1B9_SL1344, pSLT_SL1344, Chromosome,  ...<br>Genome: gi|378448274|ref|NC_016856.1|, 
INFO [2017-06-06 12:50:11,840] [GenomeManager.java:145]  Loading genome: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3
INFO [2017-06-06 12:50:11,884] [FastaUtils.java:66]  Creating index file at V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3.fai
ERROR [2017-06-06 12:50:11,915] [MessageUtils.java:64]  Could not create index file: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3.fai
org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3<br>Fasta file has uneven line lengths in contig null
	at org.broad.igv.feature.genome.FastaUtils.createIndexFile(FastaUtils.java:94)
	at org.broad.igv.feature.genome.GenomeManager.loadFastaFile(GenomeManager.java:290)
	at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:167)
	at org.broad.igv.ui.IGV.loadGenome(IGV.java:686)
	at org.broad.igv.ui.IGV.loadGenome(IGV.java:667)
	at org.broad.igv.ui.IGV.doLoadGenome(IGV.java:635)
	at org.broad.igv.ui.IGVMenuBar$11.actionPerformed(IGVMenuBar.java:550)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395)
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190)
	at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
	at java.awt.Component.processMouseEvent(Component.java:6533)
	at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
	at java.awt.Component.processEvent(Component.java:6298)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4889)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
	at java.awt.Container.dispatchEventImpl(Container.java:2280)
	at java.awt.Window.dispatchEventImpl(Window.java:2746)
	at java.awt.Component.dispatchEvent(Component.java:4711)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
ERROR [2017-06-06 12:50:11,915] [MessageUtils.java:74]  Could not create index file: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3.fai
INFO [2017-06-06 12:50:15,534] [GenomeManager.java:192]  Genome loaded.  id= V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.gff3
INFO [2017-06-06 12:50:30,049] [IGV.java:1700]  Loading 1 resources.
INFO [2017-06-06 12:50:30,049] [TrackLoader.java:120]  Loading resource, path V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam
INFO [2017-06-06 12:50:30,049] [MessageUtils.java:74]  <html>File: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam<br>does not contain any sequence names which match the current genome.<br><br>File: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pRSF1010_SL1344, pCol1B9_SL1344, pSLT_SL1344, Chromosome,  ...<br>Genome: 
INFO [2017-06-06 12:54:11,056] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-06 12:54:12,337] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-06 12:59:00,474] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-06 13:01:12,844] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-06-06 13:01:12,844] [Main.java:134]  Java 1.8.0_101
INFO [2017-06-06 13:01:12,844] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-06-06 13:01:12,844] [Main.java:136]  OS: Windows 10
INFO [2017-06-06 13:01:14,510] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-06-06 13:01:21,511] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-06-06 13:01:21,511] [Main.java:134]  Java 1.8.0_101
INFO [2017-06-06 13:01:21,511] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-06-06 13:01:21,511] [Main.java:136]  OS: Windows 10
INFO [2017-06-06 13:01:22,434] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-06-06 13:01:24,956] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-06 13:01:26,622] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-06 13:01:26,774] [CommandListener.java:106]  Listening on port 60151
INFO [2017-06-06 13:01:32,613] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-06 13:01:34,042] [GenomeManager.java:192]  Genome loaded.  id= hg38
ERROR [2017-06-06 13:01:34,211] [CommandListener.java:124]  java.net.BindException: Address already in use: JVM_Bind
INFO [2017-06-06 13:01:49,994] [GenomeManager.java:145]  Loading genome: V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\BWAIndex\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.dna.genome.fa
INFO [2017-06-06 13:01:49,994] [FastaUtils.java:66]  Creating index file at V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\BWAIndex\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.dna.genome.fa.fai
INFO [2017-06-06 13:01:50,093] [GenomeManager.java:192]  Genome loaded.  id= V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\BWAIndex\Salmonella_enterica_subsp_enterica_serovar_typhimurium_str_sl1344.GCA_000210855.2.22.dna.genome.fa
INFO [2017-06-06 13:02:27,767] [IGV.java:1700]  Loading 1 resources.
INFO [2017-06-06 13:02:27,767] [TrackLoader.java:120]  Loading resource, path V:\lab share\BORCHERT\salmonella\Shivam_2016\otogenetics raw\mapping_adapter_removed\Index3_OtA2461_combined_adapter_removed_Glen.Borchert_600-111_smRNA-Seq_8M_04132014_sorted.bam
INFO [2017-06-06 13:13:55,998] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-06 13:13:57,294] [GenomeManager.java:192]  Genome loaded.  id= hg38
INFO [2017-06-06 13:13:57,318] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-06-06 13:13:57,318] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-06-06 13:13:57,494] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-06 13:13:58,508] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-06 13:13:58,559] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-06-06 13:13:59,875] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-06 14:37:57,824] [IGV.java:1700]  Loading 2 resources.
INFO [2017-06-06 14:37:57,825] [TrackLoader.java:120]  Loading resource, path https://s3.amazonaws.com/igv.broadinstitute.org/data/hg38/gencode.v24.annotation.sorted.gtf.gz
INFO [2017-06-06 14:37:59,754] [TrackLoader.java:120]  Loading resource, path https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/Homo_sapiens.GRCh38.80.sorted.gtf.gz
INFO [2017-06-07 13:32:53,511] [ShutdownThread.java:51]  Shutting down
INFO [2017-06-07 15:57:34,789] [Main.java:133]  Startup  IGV Version 2.3.83 (132)10/18/2016 03:01 AM
INFO [2017-06-07 15:57:34,789] [Main.java:134]  Java 1.8.0_101
INFO [2017-06-07 15:57:34,790] [Main.java:135]  Default User Directory: C:\Users\Borchert\Documents
INFO [2017-06-07 15:57:34,790] [Main.java:136]  OS: Windows 10
INFO [2017-06-07 15:57:36,266] [Main.java:184]  A later version of IGV is available (2.3.93)
INFO [2017-06-07 15:57:46,292] [GenomeManager.java:145]  Loading genome: C:\Users\Borchert\igv\genomes\hg38.genome
INFO [2017-06-07 15:57:47,757] [GenomeManager.java:192]  Genome loaded.  id= hg38
ERROR [2017-06-07 15:57:47,882] [CommandListener.java:124]  java.net.BindException: Address already in use: JVM_Bind
INFO [2017-06-07 15:58:41,630] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_BBBBB_hg38_v170517.bed
INFO [2017-06-07 15:58:41,631] [TrackLoader.java:120]  Loading resource, path C:\Users\Borchert\Desktop\Mother_of_Dragons\Gillespie\G4\5stemG4s_AAAAA_hg38_v170517.bed
INFO [2017-06-07 15:58:41,823] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/normoxiaVerySensitiveLocalSortedRmDup.bam
INFO [2017-06-07 15:58:42,068] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-07 15:58:42,460] [TrackLoader.java:120]  Loading resource, path http://borchertdatasrv.southalabama.edu/data/Gillespie_data/BAM_Files_12_12_2016/hypoxia_sortedVerySensitiveLocalRmDup.bam
INFO [2017-06-07 15:58:45,784] [HttpUtils.java:833]  Range-byte request succeeded
INFO [2017-06-07 15:59:49,287] [ShutdownThread.java:51]  Shutting down