Found the solution for this issue here we go.
Over period of time if any jobs get's cancelled or terminated Data Services Creates a huge file which is stored in it's install directory log/ .In my case these files grew so large that our default job directory folder which too is installed on same directory couldn't read or write any Abap files read from ECC. So when the ETL runs there is not enough memory to read this file. In fact even our job server went down due to this very issue. I simply deleted all logs which were accumulated over period of time and everything was back to normal.
Alternate solution:
If you have opened any of data files .dat on any log on's or session then this also leads to file cannot read pipe issue etc. kind of errors. How to know this? Go and try to modify the file it will show error that it has opened in some session by some user etc. Close all sessions, delete this .dat file and re run your ETL. Everything should be good after that.
Cheers,
Sam