@isaacovercast I agree with your guess, but I'm using a public hpc cluster in our institute and not administrator. So, do you know what else ways I can do to solve my problem without administrator? Because I assume that most users are also analyzing their RADseq data in public cluster of their universities or institutes so that my problem will probably be a common problem for users willing to use ipyrad in subsequent analyses. @isaacovercast and @eaton-lab , could I occupy few more minutes of yours that help me in this problem? Besides, I also find that the same problem is happened in other subsequent analyses basing on the assembly results of ipyrad, which including tetrad, structure, treemix and BPP. I only can get results following commands of RAxML and ABBA-BABA admixture inference in the Eaton & Ree (2013) single-end RAD data set.