Hi @l.hughes, this error is caused when mafft tries to use more memory than is available on your machine and its process gets killed. We think this issue is caused by a memory leak in mafft. The best workaround for now is to switch from mafft to our nextalign tool. @rneher has written a guide for making this switch to nextalign.
Would you be willing to try out this alternate approach and let us know how it works for you?