Pipeline (Pypiper) returns error, but individual command works fine
Slurm is killing the process because it's using more memory per core than the default allocation (that's what slurmstepd: error: Exceeded step memory limit at some point means). I've never used pyPiper (like seemingly most people, I use snakemake), but presuming that you have it running either srun or sbatch at some point then specify something like --mem-per-cpu 10G.