What your awk is doing doesn't seem to fully match what your input file looks like (i.e. you're using | as a field separator, when the path is / separated, there is nothing ending with ".atr" - since everything in your input file ends with /, which means $(NF-1) returns the last useful field, not $NF)
(I didn't test the mkdir itself, but replacing it with echo gives the output I think you were looking for - assuming it's the whole path you wanted to create)