diff --git a/PTL2/run_eukphylo.sh b/PTL2/run_eukphylo.sh
index f0f0c73..6db85bd 100644
--- a/PTL2/run_eukphylo.sh
+++ b/PTL2/run_eukphylo.sh
@@ -7,52 +7,9 @@
 ## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
 
 
-## SLURM-SPECIFIC SETUP BELOW
-
-#SBATCH --job-name=EukPhylo # Job name
-#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 --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 -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
-module load ETE
-module load Biopython/1.79-foss-2021b
-module load DIAMOND/2.0.13-GCC-11.2.0
-module load MAFFT
-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
-module load Guidance_mid #Smith College HPC specific
-
-#export PATH=$PATH:/Path/To/Executable/Files
-
-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 > Output.out
-
-# 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} 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!
-
-
-
+python3 Scripts/eukphylo.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder > Output.out