Syntax of the inputs for LightGBM binary build (without python API)
The first column in the input file is considered to be the target variable. I found this by trial and error.

EDIT

There is a parameter called label_column which can take an integer value from 0 to N, to specify which column is the target variable. (source: https://lightgbm.readthedocs.io/en/latest/Parameters.html)