There are two possibilities.
You forgot to put the %id% in the jstack call.
jstack %id% > jstack.txt
So the whole correct batch file should be:
@echo off
set /p id=Enter ID:
echo %id%
jstack %id% > jstack.txt
And/Or 2. You did put it in the code (and forgot to tell us in the question) but when you ran the batch file you hit the Enter key instead of typing an ID (say 1234).
What's happening is the result of these two mistakes:
jstack is supposed to be called with the id that you supply it.
But in your case (according to the code you supplied in the question) you called it without any variable. You wrote:
jstack > jstack.txt
So when you run jstack with no variable it outputs the following:
Terminate batch file Y/N?
Your second mistake is that you pressed Enter instead of giving a value when the program asked you: Enter ID:. If you would have put in an ID at this point, say 1234, the %id% variable would become that value, in our case 1234. But you did NOT supply a value and instead pressed Enter. When you don't give the variable any value, and if that variable was not set to anything else before, then the variable %id% is set to the prompt of the set command!! So now %id% is set to Enter ID: which was echoed on your screen as requested in the batch file BEFORE you called the jstack.
But I suspect you DID have the jstack %id% > jstack.txt in your batch file code with the %id (and omitted it by mistake from the question), and that you hit enter without typing in an id. The batch program then echoed the id, which is now "Enter ID:", and then ran jstack Enter ID: > jstack.txt
Jstack itself echoed the input, encountered a mistake and asked to terminate.
And all this was written into the jstack.txt file.