Hi again Deren and Isaac. As Nitish Narula, my ipyrad run is going to be canceled by the scheduler on the cluster in a few days due to time limits. In my case, I am running step 3. When I used pyRAD, I repeated this step independently only with the samples which could not finish the clustering within samples and then I added these last samples to the clust.XX folder. Can I do the same with ipyrad? Is it going to affect to the stats files or any following steps? Or maybe I could restart the analysis again and continue with the samples which did not finish step 3, is it possible? Thanks you in advance!!