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IQ-TREE stuck without error code when constraint tree is provided #253

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rramosbaez opened this issue Nov 9, 2023 · 0 comments
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@rramosbaez
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When I run IQ-TREE to produce a ML phylogeny using the command below, it creates it easily within an hour:
"./iqtree
-s CX.MSA.fasta
-alrt 1000
-m JTT+G+F
-nt AUTO"
When I add my constraint tree to this command, "-g constraint_CX.newick" the code quickly runs up to and stays stuck at the point below.
"Reading constraint tree constraint_CX.newick...
Creating fast initial parsimony tree by random order stepwise addition..."
I have run it up to four hours to see if it eventually moves forward, but to no avail. I have no warnings in my log, much less errors. What might be happening?

I have tried changing the file format (from .tre to .newick), ensured sequence names were formatted correctly, and made sure the tree had no root.

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