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When I use batchfile.bat >> logfile.txt command in the Windows commandline, it correctly outputs the normal output into the text file, but the Java exceptions get output to the console. Can I make it so that exceptions are written to log file as well?

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Java exceptions are printed on the standard error stream.

To pipe the standard error stream (file descriptor 2) into a file you can do:

batchfile.bat 2>> errorlog.txt

To pipe both standard error and standard out into the same file:

batchfile.bat >> logfile.txt 2>&1

You can do the same on Unix and Windows

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