Eclipse giving error "database disk image" is malformed.

Ia m using sqlite 3 db. The size of db has grown to 2GB. It was working fine. Suddenly the eclipse started giving error while inserting data:

java.sql.SQLException: database disk image is malformed
    at org.sqlite.DB.throwex(DB.java:288)
    at org.sqlite.NestedDB.prepare(NestedDB.java:115)
    at org.sqlite.DB.prepare(DB.java:114)
    at org.sqlite.PrepStmt.<init>(PrepStmt.java:37)
    at org.sqlite.Conn.prepareStatement(Conn.java:224)
    at org.sqlite.Conn.prepareStatement(Conn.java:217)
    at org.sqlite.Conn.prepareStatement(Conn.java:206)
    at application.loginModel.interactWithDB(loginModel.java:205)
    at application.loginController.buttonAction(loginController.java:30)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at sun.reflect.misc.Trampoline.invoke(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at sun.reflect.misc.MethodUtil.invoke(Unknown Source)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(Unknown Source)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(Unknown Source)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
    at com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
    at javafx.event.Event.fireEvent(Unknown Source)
    at javafx.scene.Node.fireEvent(Unknown Source)
    at javafx.scene.control.Button.fire(Unknown Source)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
    at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(Unknown Source)
    at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(Unknown Source)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
    at com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
    at com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
    at javafx.event.Event.fireEvent(Unknown Source)
    at javafx.scene.Scene$MouseHandler.process(Unknown Source)
    at javafx.scene.Scene$MouseHandler.access$1500(Unknown Source)
    at javafx.scene.Scene.impl_processMouseEvent(Unknown Source)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$355(Unknown Source)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
    at com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
    at com.sun.glass.ui.View.notifyMouse(Unknown Source)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$null$149(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

EDIT: I opened sqlite CLI and did

pragma integrity check;

and CLI status shows:

*** in database main ***
Page 65526 is never used
Page 65527 is never used
Page 65528 is never used
Page 65529 is never used
Page 65530 is never used
Page 65531 is never used
Page 65532 is never used
Page 65533 is never used
Page 65534 is never used
Page 65535 is never used
Page 65536 is never used

What has went wrong?