Chrome native messaging - disconnected when launching another app - google-chrome

What I'm trying to do?
I am trying to write an application based on such schema:
The chrome extension launches an application (.jar file) on my computer
The application launches another application (external, not written by me), I am passing data to it, it displays the window for user, user enters some data to it, and then this app returns the data to the parent app
The parent app processes the child app response and sends it back to the chrome extension
What's wrong?
When the window of the child app is displayed, the chrome extension is disconnected (it happens exactly at the same time). What follows, the result is not going back to the chrome extension.
What works:
If I omit point no. 2 (just mocking the answer from the child app), the result is returned to the chrome extension.
Including all points: the child app returns it's result correctly. The parent app catches it and tries to return it to the chrome extension (not succeeding, the extension is disconnected)
Also tried
I tried to do it using java multithreading (ExecutorCompletionService, Callable, Future), I wanted to launch the child app in a separate thread and block the main thread until the child is finished, it didn't help.

Solved!
The communication between the chrome extension and my app is through the standard input/output. Somewhere in the code of my app (written in java) there was System.out.println called. It made some mess on STDOUT and made the app disconnect from the extension. It happened in the same time with launching the external app as I saw it, probably didn't happen exactly at the same time, but some time before/after, something the person cannot see.
Multithreading has nothing to do with this problem.
Solution
I found and removed all code writing to standard output

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