Hi Nick,
popabc creates the .rej file and then it will write there as soon as
the buffer fills up or the program terminates successfully (i.e.
without errors). My guess is that the program didn't run successfully
because of errors on the .prs, .ssz or .sst files.
using the example provided successsfully can give you better insights
on how to use popabc.
best,
Joao