The (user level) run command does not record a jobid in a segment's properties.ini file which means one cannot eg restart from a checkpoint since simfactory complains about an unset jobid:
simfactory/bin/sim create-run test1 --parfile par/tov_ETK_2018_lisbon.par --procs 1 --walltime 0:5:0 & grep jobid ~/simulations/test1/output-0000/SIMFACTORY/properties.ini
shows the issue (but not producing any output). And the error obtained when trying to restart is along the lines of
Simulation name: binarybh9 Error: job id is negative Aborting Simfactory
This was reported by Qingwen Wang in http://lists.einsteintoolkit.org/pipermail/users/2018-September/006524.html
A workaround is to not use run as a user but always submit or to use the cleanup command after which simfactory is fine with there not being a job id.