I wanted to try out cmaple and set --pathogen-force. However, only after wondering why the logs looked so familiar (like normal iqtree2 ones) did I notice that cmaple didn't run.
It's easy to miss that single line in the quite verbose logs:
WARNING: This version was not compiled with CMAPLE integrated. Running IQ-TREE algorithm...
See what my logs look like (the first 40 lines, there are 300 more):
I would suggest that iqtree2 errors when --pathogen-force is set but iqtree isn't compiled with cmaple support. If you force something, but it's not possible, I would expect an error, not just a warning and otherwise falling back.
Also, it would be good to not display the cmaple options in the iqtree2 -h help output if cmaple isn't supported.
Is there a simple way to test for cmaple support other than setting --pathogen-force and checking for the warning line in the logs?
I wanted to try out cmaple and set
--pathogen-force. However, only after wondering why the logs looked so familiar (like normal iqtree2 ones) did I notice that cmaple didn't run.It's easy to miss that single line in the quite verbose logs:
See what my logs look like (the first 40 lines, there are 300 more):
I would suggest that iqtree2 errors when
--pathogen-forceis set but iqtree isn't compiled with cmaple support. If you force something, but it's not possible, I would expect an error, not just a warning and otherwise falling back.Also, it would be good to not display the cmaple options in the
iqtree2 -hhelp output if cmaple isn't supported.Is there a simple way to test for cmaple support other than setting
--pathogen-forceand checking for the warning line in the logs?