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Thanks Chris for your response!
Do I need to add an Each Pipe in every sub assembly to fetch the counters per sub assembly? Is that what you mean by "prefixing your counter group with the SubAssembly name (as implied below), and retrieving the counter for the SubAssembly" in your reply?
I have tried by adding Counter function in each subassembly as below:
pipe = new Each(pipe,new Counter("SubAssemblyName", "SubAssemblyId", 1));
But adding an each pipe in every sub assembly takes more time to run a job. Every time I will be having huge data for processing. I had tried to run the job on my sample data (~ 1GB) with 8-10 subassemblies were used for data processing and I found that difference in execution time was noticeable.