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.
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.