Can't align 2 sequences, (MAFFT killed)
--thread 4 is essential, --maxiterate just try and get it working, not getting it to work optimally. Just make sure there are no other processes running on the machine when --thread 4 is operating, e.g. you are using another machine as your desktop
The gist is as you spread the calculation across your processors (4) and simplify the calculation (lowering the iterations), you are getting further into the calculation, for example now you are getting into gap penalties.
If you are agreed then I would try performing the alignment using just one chromosome of the human genome against the chimp genome and I suspect that would work. Then take it from there.
The objective is to get the calculation working, for example I wouldn't trust a result with max. iterations of 2, but once you have it working you can then start refining the parameters towards optimal results. The i3 processor isn't perfect in context.
Using --thread 4 is super important and you want to increase maxiterate towards the default if the machine supports it.
I suspect the solution is to perform the calculation on an 8+-core machine and set --thread 8 (or higher depending on the number of cores on the machine), at least it will get further into the calculation. With 4-cores and an i3 (diagnostics of RAM usage would be nice) in any case it just doesn't seem to like it. The alternative is to perform this across the genome via sampling the chromosomes on your current i3.

Just to explain why this works. When you have a RAM intensive job and you spread it across cores the RAM overhead massively reduces for each core that is added. Don't ask me how this works in the hardware mecahanics of RAM distribution per core. The reason I know this is because of emperically parallelising Bayesian calculation using each chain on a different core.