diff --git a/PTL2/run_eukphylo.sh b/PTL2/run_eukphylo.sh
index b63c485..fa39157 100644
--- a/PTL2/run_eukphylo.sh
+++ b/PTL2/run_eukphylo.sh
@@ -1,4 +1,4 @@
-## Last updated Jan 2025 by Auden Cote-L'Heureux
+## Last updated Jan 2025 by Auden Cote-L'Heureux; modified Feb 2025 by Adri K. Grow
 
 ## This shell script is used for running EukPhylo part 2, and includes a general setup for use on an HPC that uses 
 ## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the 
@@ -6,7 +6,7 @@
 ## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
 
 
-#!/bin/bash
+#!/bin/bash ## DELETE all lines before this to run
 
 ## SLURM-SPECIFIC SETUP BELOW
 
@@ -14,11 +14,16 @@
 #SBATCH --output=Run_EukPhylo.%j.out # Stdout (%j expands to jobId)
 #SBATCH --nodes=1
 #SBATCH --ntasks=10 ## On the Smith College HPC (Grid), we have to change this to be double the number of task/batches you want to launch
-#SBATCH -c 24 # Number of Cores per Task
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=email@xxx.edu ##add your email address for job updates
+
+## UMass HPC (Unity) requirements below (DELETE section if not applicable):
 #SBATCH --mem=125G # Requested Memory
-#SBATCH -q long # Partition. Only use this on certain HPCs (e.g., Unity at UMass).
+#SBATCH -c 24 # Number of Cores per Task
+#SBATCH -q long # Partition
 #SBATCH -t 336:00:00 # Job time limit
 
+#Load required modules
 module purge       #Cleans up any loaded modules
 module use /gridapps/modules/all    #make sure module locations is loaded
 module load slurm
@@ -30,20 +35,22 @@ module load RAxML
 module load IQ-TREE/2.1.2-gompi-2021b
 module load tqdm/4.64.1-GCCcore-12.2.0
 module load Python/3.9.6-GCCcore-11.2.0
-export PATH=$PATH:/Path/To/Executable/Files
+module load Guidance_mid #Smith College HPC specific
 
-parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders
+#export PATH=$PATH:/Path/To/Executable/Files
 
-## RUN COMMANDS BELOW
+parent='/Your/Home/Folder/' # The folder where you are running EukPhylo (this should contain the Scripts and input data folders)
+
+## EXAMPLE RUN COMMANDS BELOW
 
 # A simple run of part 2, starting from ReadyToGo files and running through tree building
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list  ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder
+srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder > Output.out
 
-# Another example run starting from ReadyToGo files and running through tree building, with the commonly used similarity filter cutoff, blacklist, and  "sim_taxa_list" arguments (see Wiki)
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list  ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder --similarity_filter --blacklist ${parent}Blacklist.txt --sim_cutoff 0.99 --sim_taxa sim_taxa_list.txt
+# Another example starting from ReadyToGo files and running through tree building, with the commonly used similarity filter cutoff, blacklist, and  "sim_taxa_list" arguments (see Wiki)
+srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start raw --end trees --gf_list ${parent}listofOGs.txt --taxon_list ${parent}taxon_list.txt --data ${parent}Input_folder --output ${parent}Output_folder --similarity_filter --blacklist ${parent}Blacklist.txt --sim_cutoff 0.99 --sim_taxa sim_taxa_list.txt > Output.out
 
 # An example of running just the concatenation step of part 2, starting from trees
-srun --exact -n 1 -D ${parent} python eukphylo.py --start trees --concatenate --concat_target_taxa Sr_rh --data Output
+srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --start trees --concatenate --concat_target_taxa Sr_rh --data ${parent}Output > log.out
 
 # See the Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop) for more details!