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Bug: No way to avoid ERROR: Initial tree is not compatible with constraint tree
#144
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Thanks a lot for the quick response!
I think I somehow managed to workaround the issue for now. So it's not
urgent.
I wrote a script that tells me which splits in the parsimony tree (found it
in outdir) are not in the constraint tree (~600 terminals) and found
something.
When I pruned that split, things worked again. Not 100% sure that that was
it.
It's entirely possible I'm somehow feeding in a bad tree that makes no
sense and that it's just the log/error output that needs to be clearer.
In general, more verbose output for errors like this would be super useful.
When you have big trees, manual inspection is a hopeless task, so if Iqtree
could spit out more of it's internal state when something errored that
would be amazing.
…On Tue, Sep 26, 2023, 23:12 roblanf ***@***.***> wrote:
Hi Cornelius,
@bqminh <https://github.com/bqminh> @thomaskf
<https://github.com/thomaskf> and I have a meeting today and I'll bring
this up. Hopefully we can get a solution to you quickly!
Rob
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Just hit this issue again. I wish I had copied that script here. I'll give you full repro details again for testing in case someone has a look at this part of the code: iqtree2 -ntmax 1 -s builds/wuhan/masked_recombinant_XBB-delim.fasta -m GTR \
-ninit 2 -n 2 -me 0.05 -nt AUTO -redo -czb \
-ninit 1 -n 1 -g builds/wuhan/pruned_constraint_XBB.nwk \
> builds/wuhan/masked_recombinant_XBB-delim.iqtree.log
All input/output files are in this archive: Edit: I found the script and added it as a Gist here for others to use in case they also encounter this error: https://gist.github.com/corneliusroemer/0b49aac048e6ba404388ba0ae829691e My script doesn't find any disagreement between constraint tree and parsimony tree, strange. It's of course possible the script is wrong: python scripts/constraint_detector.py builds/21L/pruned_constraint_XBB.nwk builds/21L/masked_recombinant_XBB-delim.fasta.parstree
[] |
Hitting this issue again, new tree, again can't find any disagreement between provided constraint tree and parsimony tree. Now v2.2.6
(txt extension is so I can upload it here) Update: Upon closer inspection I found an issue in my constraint tree. I had labelled an internal node JN.1.2 but that was also a real sequence given to the tree builder. Hence the incompatibility, I presume. Constraint looked something like this:
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Hi @corneliusroemer, |
Thanks a lot for IQtree! I use it to make reference trees for Nextclade.
I use a pretty sophisticated constraint tree to avoid homoplasies pulling together branches I know should be separate.
I now get an error that's quite frustrating as there seems to be no clear workaround and it's almost impossible to debug giving limited logging:
ERROR: Initial tree is not compatible with constraint tree
This feels like a bug as the initial tree should be built to be compatible with whatever constraint tree I pass in. There should be a way to build an initial tree just from parsimony addition to the constraint tree - that way the constraint would always be satisfied.
If that's hard to implement, at least better logging would be very useful: if you could output which part of the constraint tree is violated, and if it was possible to output the initial tree so that I could inspect in a treeviewer, that'd be super amazing.
Here are all the necessary files to reproduce.
Command I run:
Files are in here (just get rid of .txt ending and untar, the txt is necessary to be able to upload here): constraintbug.tzst.txt
Version:
$ iqtree2 -v IQ-TREE multicore version 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
From logs:
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