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getRuntime question

 
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I have a binary from another company I kick off within my java program that is supposed to write to a log file. It creates the log file, but does not show anything to the screen. If I add redirecting of stderr to stdout (i.e., 2>&1) to the command I run, I see I am guessing stderr lines to my stdout, but the log does not get anything added until around 4099 bytes. If I run the command normally outside of my program by the way it writes to the log immediate and to stdout. Am I using the wrong method to display lines the lines from getRuntime? Here is a snippet of code I use:
 
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