@isaacovercast thanks for your reply- I would also have thought I could run it on my laptop (Intel i7 with 8GB RAM), however, it completely takes over my computer and runs forever. I am worried that I have something wrong in my param file? However the only things I changed were: the assembly name in line , the path to my files on line  - they are already sorted and barcodes removed, the datatype (mine are ddrad) on line , the restriction overhang in line  (to TGAC, AATT) and the output files I want in line . Step three just keeps going and going and going - I can see that temporary files are being made and it does eventually get there for some of the individuals, but I have not managed to get to the end of this step as it takes too long, hence trying to get it to work on the HPC. Is this normal? Any suggestions? Also, is there a way to restrict the number of cores that it uses (I have 4 and it seems to automatically use all of them, meaning I can't do anything else on my computer while it is running as it slows down to a crawl). I know there was a way to do this in pyrad from my limited experience in pyrad before discovering ipyrad. Thanks again for your help.