diff --git a/PTL2/Scripts/contamination.py b/PTL2/Scripts/contamination.py
index 10608bf..221e7fe 100644
--- a/PTL2/Scripts/contamination.py
+++ b/PTL2/Scripts/contamination.py
@@ -341,9 +341,9 @@ def cl_iqtree(params):
 			tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
 			os.mkdir(tax_iqtree_outdir)
 			os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --prefix ' +  tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')	
-		#Copy over the final output
-		if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
-			os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
+			#Copy over the final output
+			if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
+				os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
 
 	
 #Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method)
@@ -355,9 +355,9 @@ def cl_iqtree_fast(params):
 			tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
 			os.mkdir(tax_iqtree_outdir)
 			os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --prefix --fast ' +  tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')	
-		#Copy over the final output
-		if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
-			os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
+			#Copy over the final output
+			if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
+				os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
 
 
 #Wrapper script to manage parameters and iteration