From ff249d79731a380d2d19dcb795e186b423fa7232 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Tue, 6 May 2025 11:08:50 -0400 Subject: [PATCH] Update trees.py --- PTL2/Scripts/trees.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/PTL2/Scripts/trees.py b/PTL2/Scripts/trees.py index a555525..ae2776c 100644 --- a/PTL2/Scripts/trees.py +++ b/PTL2/Scripts/trees.py @@ -44,9 +44,9 @@ def run(params): #Run IQ-Tree if params.tree_method == 'iqtree': - os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree') + os.system(' /usr/local/bin/iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree') elif params.tree_method == 'iqtree_fast': - os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --fast --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree') + os.system('/usr/local/bin/iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --fast --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'):