About runing Pilon on individual chromosomes when polish draft genome assembly

Hi all,

Recently I have been working on genome assembly for several species on my own server (1TB ram, 128cores, and enough internal storage). My problem is that when the estimated genome size is more than 2.5GB, the PILON software which is used for polish draft genome assembly was stopped because of insufficient memory.

One of my solutions is to split the whole draft genome assembly by chromosomes followed by polish by PILON, then concentrate the polished chromosomes into a big one. Here I want to know any possible issues by doing in this way.

Thanks,