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--- sepp-software [2021/12/28 13:39] – aorth
+++ sepp-software [2021/12/28 13:49] (current) – aorth
@@ Line 17: / Line 17: @@
 <code>$ module load sepp/4.5.1
-$ run_sepp.py</code>
+$ run_sepp.py -h</code>
+The general command for running SEPP is:
+<code>run_sepp.py -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size></code>
+**Note:** please use the "-x" or "--cpu" options to set the number of CPUs for your SEPP run. This number should match the number of CPUs requested in your SBATCH allocation.
 ===== Installation ======