From 2173eda5a00182f69d6958a0fbd4d86be718c81a Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:34:37 -0500
Subject: [PATCH] Update run_eukphylo.sh

---
 PTL2/run_eukphylo.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PTL2/run_eukphylo.sh b/PTL2/run_eukphylo.sh
index 21872ff..2240300 100644
--- a/PTL2/run_eukphylo.sh
+++ b/PTL2/run_eukphylo.sh
@@ -28,7 +28,7 @@ module load Python/3.9.6-GCCcore-11.2.0
 export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
 parent='/beegfs/fast/katzlab/' #add your path starting with the name of your folder, should begin with /beegfs/fast/katzlab/
 #if you are running batches, you need an srun line for each batch!
-srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.py --similarity_filter --sim_cutoff 0.95 --sim_taxa sim_taxa.txt --blacklist GuidanceRemovedSeqs_allConservedRuns_ML_nov_dec_2023.txt --start raw --end trees --gf_list B1_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B1 > Output_folder_B1.out &
+srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.95 --sim_taxa sim_taxa.txt --blacklist GuidanceRemovedSeqs_allConservedRuns_ML_nov_dec_2023.txt --start raw --end trees --gf_list B1_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B1 > Output_folder_B1.out &
 wait
 ###Grid end
 
@@ -45,6 +45,6 @@ module load conda/latest
 conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/
 parent='/work/pi_lkatz_smith_edu/' #add your path startin>
 #if you are running batches, you need an srun line for each batch!
-srun -D ${parent} python3 ${parent}Scripts/phylotol.py --similarity_filter --sim_cutoff 0.99 -->
+srun -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.99 -->
 wait
 ###Unity end