As shown in the visualization above, Snakefile contains dependent rules for the sub-directory. Each rule corresponding to a shell command. If you see any error that occurs during the execution of snakemake on qsub or sbatch, you need to read the stderr and find out which command/rule is the reason causing failure. You can then copy the command and analyze the error information. You may execute that command again locally (or via a separate job) to see if it reoccur.