Joyce,
Sorry that you are seeing this issue. The ‘Run EJB Deploy Tool’ option is for Websphere 6.1/Websphere 7. The latest version of MyEclipse (10.7) has support for Websphere 6.0.
I strongly recommend switching to the latest version of MyEclipse i.e 10.7, to take advantage of over 4-5 years of development time and enhancements we made since 8.6 release.
You can check to see if these steps help resolve your issue :
1)Make sure the Add line numbers attribute is set for the project and general compile preferences.
2)Unchecking the Add line numbers attribute, click apply, re-enable it, click apply and try again
3) Make sure the server running in debug mode.
a.Window -> preferences -> MyEclipse -> Servers -> Websphere -> Websphere 6.0
b.Select your profile and hit “Edit”
c.Hit next twice
d.Are you using a JDK or JRE (if you are using a JRE, try switching to a JDK)?
4) If you are running in debug mode on a JDK:
a.Go to your workspace directory outside of MEB and go to .metadata\.plugins\org.eclipse.core.runtime\.settings
b.Open org.eclipse.jdt.core.prefs with ultraedit
c.Add this line to the bottom of the file
org.eclipse.jdt.core.compiler.debug.lineNumber=generate