Non-comprehensive constraint tree issue

[zcalamari]

Hello,

I am trying to run RAxML-ng with a non-comprehensive constraint tree, but I keep getting this error:

[00:00:00] Loaded non-comprehensive constraint tree with 15 taxa
Assertion failed: (bin_tree->inner_count == old_inner_count + degree-3), function pllmod_utree_resolve_multi, file /Users/sco/alexey/raxml-ng/libs/pll-modules/src/tree/pll_tree.c, line 356.
zsh: abort /Applications/raxml-ng_v0.9.0_macos_x86_64/raxml-ng --all --tree-constraint

I have also tried running this on the CIPRES implementation and it also quits after the "[00:00:00] Loaded non-comprehensive constraint tree with 15 taxa" line. My constraint tree is a fully bifurcating newick tree that doesn't have all the species in it.

Any help would be appreciated!

[amkozlov]

could you please post your constraint tree file and full raxml-ng log here?

[zcalamari]

I have attached both, thanks!

RAxML.output.txt

NewickExtantCollapsedBackboneTree.txt

[amkozlov]

For some reason, your tree had an extra pair of parenthesis around of the clades. Please find fixed tree attached.

Also, I strongly recommend to upgrade raxml-ng to the most recent version.

tree3.txt

[zcalamari]

Thanks for the support! I was planning to run this on CIPRES and was using my local install to troubleshoot when the CIPRES version wasn't working. Will update regardless.

[amkozlov]

OK from now on, raxml-ng will print a meaningful error message in such cases.

So I guess this issue is resolved?

[zcalamari]

Yes, thank you!