As long as every program started by run.bat just writes to STDOUT and STDERR, you can even use a "pipe open" and read the output directly, without messing with temporary files and without fighting the race conditions that come with them:

open my $pipe,'run.bat |' or die "Ooops: $!";
while (my $line=<$pipe>) {
    print $line; # <-- stupid example
}
close $pipe;
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Note that this example catches only STDOUT, not STDERR. If you want both in ONE stream (that may become very hard to "unmix"), use output redirection:

open my $pipe,'run.bat 2>&1 |' or die "Ooops: $!"; 
# ...
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If you want only STDERR, use that, plus get rid of STDOUT (write to the null device, i.e. NUL on DOS/Win, /dev/null on Unix):

open my $pipe,'run.bat 2>&1 >nul |' or die "Ooops: $!"; 
# ...
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If you want both streams separately, use IPC::Open3 or similar.

Also note that you probably don't need the wrapping batch file, you can also start the java runtime executable directly, typically java.exe -jar jarfile.jar arg1 arg2:

open my $pipe,'java.exe -jar jarfile.jar arg1 arg2 |' or die "Ooops: $
+!";
# ...
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Alexander