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Update trees.py

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Godwin N. Ani 2025-05-06 11:08:50 -04:00 committed by GitHub
parent 1d7d8b9e91
commit ff249d7973
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1 changed files with 2 additions and 2 deletions
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PTL2/Scripts/trees.py
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@ -44,9 +44,9 @@ def run(params):
#Run IQ-Tree #Run IQ-Tree
if params.tree_method == 'iqtree': 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': 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 #Copy over the final output
if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'): if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):