Thanks for the suggestion Tom. Running the DependentsToHTML.cmd directly helped me to narrow down the issue. I got the below exception during the execution.
Exception in thread "main" java.lang.RuntimeException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: depfind.sourceforge.net
I believe, the application was trying to access some contents over the INTERNET and got blocked by firewall. I applied some proxy settings to by-pass this issue and the MAT tool was working fine for me.. It would be very much helpful if the exception handling was smart enough to report this issue during the initial run itself.
The following changes should be applied to run.cmd, for those who are getting similar firewall issue. Please get the proxy details from your System Admin.
"-Dhttp.proxyHost=<proxy host> -Dhttp.proxyPort=<proxy port>"
set DEPENDENCYFINDER_OPTS=-Xms512m -Xmx1024m -Dhttp.proxyHost=<proxy host> -Dhttp.proxyPort=<proxy port>
java -Xms512m -Xmx1024m -Dhttp.proxyHost=<proxy host> -Dhttp.proxyPort=<proxy port> -cp "%CP%" -Dredhatlogdir="%LOGDIR%" -Dconfig.xml="%CONFIG_XML%" com.mwc.mat.ToolMain