Data analysis-Not enough RAM issue

Hello All,

I have sequence data from four MiSeq V3 runs and am analyzing it using a machine with 64GB RAM and 1 TB hard drive capacity. I can run the commands up to unique.seqs. However, when I run the next command, pre.cluster, the computer runs out of RAM and the analysis stalls can not proceed any further. I was wondering, if the sequence data can be analyzed in batches (I have data from four sequencing runs), one run at a time and then the final output files (shared file) be combined for the final analysis?

Thank you.