It have been reported that the tree module runs forever when building with IQTree in consensus mode.
After further check, I found the ModelFinder process is quite time-consuming (usually take > 2 hours) even with single MSA file. Haven't tested RAxML but I suspect it also takes similar time to process. In this case, building trees from all the MSAs with IQTree/RAxML in consensus mode seems to be unrealistic.
Potential resolutions:
- Looking for parameters that can speed up IQTree/RAxML and apply it when using consensus mode.
- Removing IQTree and RAxML from consensus mode.
It have been reported that the tree module runs forever when building with IQTree in consensus mode.
After further check, I found the ModelFinder process is quite time-consuming (usually take > 2 hours) even with single MSA file. Haven't tested RAxML but I suspect it also takes similar time to process. In this case, building trees from all the MSAs with IQTree/RAxML in consensus mode seems to be unrealistic.
Potential resolutions: