can not run Libshuff command

I have been trying to run the Libshuff command to compare 4 communities. I have the combined distance matrix in phylip format (N1merged_trimmed.filter.phylip.dist). Each time I try reading the distance matrix in mothur, I get the following error message “Error: std::bad_alloc has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at, and be sure to include the mothur.logFile with your inquiry.”
What is going on? I was able to read bigger matrices before in mothur. the only difference is that I was not using the group option then.
One more thing. Since I have the matrix in both column and phylip formats, a quick comparison of the numbers in both was surprising. the column matrix has very small distance (the largest pairwise distance was 0.05-0.06) while all the distances in the phylip matrix were >0.1. Shouldn’t the numbers be similar?