From 0eb002a1bde640debfc891014129816f9282b471 Mon Sep 17 00:00:00 2001 From: MCLeleu <123706003+MCLeleu@users.noreply.github.com> Date: Wed, 17 Apr 2024 15:08:24 -0400 Subject: [PATCH] Update trees.py Changed -T AUTO for -T 10 on the iqtree line --- PTL2/Scripts/trees.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PTL2/Scripts/trees.py b/PTL2/Scripts/trees.py index 19a8dab..1b4df49 100644 --- a/PTL2/Scripts/trees.py +++ b/PTL2/Scripts/trees.py @@ -43,7 +43,7 @@ def run(params): os.mkdir(tax_iqtree_outdir) #Run IQ-Tree - os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T AUTO --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree') + os.system('iqtree2 -s ' + guidance_path + '/' + 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'):