lualatex: emergency stop when including a file from subfolder and setting aux/output directories

Question

I have a main file including many files from the same subfolder. I get lualatex working in case:

1. I include the files from the subfolder and let the aux/pdf files be generated in the main directory
2. I don't include any file from the subfolder and set the directories aux/output to different subfolders.

However, when I include files from the subfolder and set aux/output directories I got an error

Emergency stop. \include{SourceFiles/Ch2_Literature}

I can't write on file `SourceFiles/Ch2_Literature.aux'. \include{SourceFiles/Ch2_Literature}

where I don't understand why it looks for aux file in the subfolder instead of the aux-directory I already set.