ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'.

[rupesht]

The issue is still open please answer.

[nbo245]

The error is suggesting there might be a problem w/ the way you're reading data into the object containing your phenotype data.

Try explicitly specifying the delimiters you used in the file containing your phenotype data.

For example, if you load in your phenotype data with:
phenotype <- read.table("somefile.txt", sep=","),head= TRUE)

You'd load in a csv file with a header row at the top of the file.

Change sep="," to sep=" " or sep="\t" and the delimiter would change to a space or tab between different columns respectively.