Error in validate.lassosum.pipeline(out) : There's no variation in phenotype

[Mahantesh-Biradar]

I have a binary outcome denoted by 1 and 2 in the .fam file of test data and I'm getting the following error when I tried to run validation step:

v <- validate(out) # Use the 6th column in .fam file in test dataset for test phenotype

Error:

Error in validate.lassosum.pipeline(out) :
There's no variation in phenotype

Can you please suggest how to address this?

PS: I have replaced missing values with NA instead of -9

[privefl]

Is there any variation in this column?
Or do you have the exact same value in all entries?

[Mahantesh-Biradar]

Yes, there is a varition. I have about 14K cases and 400K controls and few missing values indicated by NA.