epilogue, for the ones interested in the resolution of this subject and you must be if you are here 
with the great help from SAP support, and by checking logs:
1.Framework log: /usr/sap/dataprovagent/log/framework.trc
2.Instance Log: /usr/sap/dataprovagent/LogReader/<instancename>/log/<instance name>.log
support found that Port number 49159 that was used in configuring the MSSQLLogReader Adapter was already used by some other application, another issue was that instance name was specified as an SQL SERVER instance name and should be a rep agent instance name and could be anything, instance administration port is a rep agent admin port and not an Sql Server instance port (not obvious from the guide), now we have some new issues, but that is another discussion
Thank you Hitesh!
