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Update trees.py

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Godwin Ani 2025-03-13 17:21:03 -04:00 committed by GitHub
parent fe79fc37e5
commit 07131fa94d
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PTL2/Scripts/trees.py
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@ -46,7 +46,7 @@ def run(params):
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')
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/iqtree -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'):