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Update trees.py

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Changed -T AUTO for -T 10 on the iqtree line
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MCLeleu 2024-04-17 15:08:24 -04:00 committed by GitHub
parent 18f4686223
commit 0eb002a1bd
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PTL2/Scripts/trees.py
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@ -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'):