The file 

metarandoXYZTRAIN .mat (format v4) or .txt

gives the groundtruth 

X Y Z (in meters) of the whale

for the first 4024 clicks of the waveform_of_the_clicks_TRAIN_TEST_sets.mat matrix
(in the same row order)

The annotation od the 2012 last clicks of the matrix is not given.

The hydrophone is at (0,0,0). 
The range of the whale is the norm(X,Y,Z).
The non click have the coordinates (-1,-1,-1), you shall predict for each test if it is a non click (then write -1 ), if it is a click you have to predict its range (norm L2 (X,Y,Z)) and/or its depth (Z) in meter.

Note that the row of the matrix are in random order ( = clicks(rando) ), as the task is not a tracking task, but range estimation on each individual click based on its multipulsed temporal structure.