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MSTRG.2is being replaced in the finaloutputfile. You are clobbering the file in each iteration, so I'd expect that only the last replacement would be visible. Just do the redirection tooutputafter the loop instead of in each iteration (just like you're already redirecting the loop's input fromtemplate). I'm not posting this as an answer since I'm not sure why you say (or how it's possible) thatMSTRG.2is being replaced.while ...; do ...; done <template >output. And redirect the twoechocalls to standard error to avoid getting them in the output:echo ... >&2.readloop at all, but do it in one pass by adapting the scheme given in the linked answer.