From a15ba2402de5ddb8cfbf03d5231b3f7cfcdb5f24 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Mon, 4 Dec 2023 14:31:45 -0500 Subject: [PATCH] Setting -T AUTO in IQ-Tree --- 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 08d13ce..6c16a1a 100644 --- a/PTL2/Scripts/trees.py +++ b/PTL2/Scripts/trees.py @@ -25,7 +25,7 @@ def run(params): tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0] os.mkdir(tax_iqtree_outdir) - os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree') + os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T AUTO --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree') 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')