concordance factor: -scfl flag does not work but -scf does

[crcardenas]

Hello,

I have had this issues running iqtree2 for concordance factors on my datasets. I would like to run the -scfl flag, but only the -scf flag works with my data.

I am running Version IQ-TREE multicore version 2.3.6 for Linux x86 64-bit built Aug 4 2024

My command is a simple for loop:

for MINTAXA in 27 33 36; do 
iqtree2 -te ethiopia_${MINTAXA}_parti.nex.best_model.nex.treefile \
-s ethiopia_${MINTAXA}min.nex \
-m ethiopia_${MINTAXA}min_parti.nex.best_model.nex \
-T 2 \
--scfl 100 ; 
done

When running this code, I get the following error:

...
Reading model parameters from file ethiopia_36min_parti.nex.best_model.nex
ERROR: Expecting a double or a distribution name, but found #nexus. Could not found the distribution named #nexus

I have tried loosing the for loop and changing the -m flag to -S (as seen in another issue: #155 ; but it is listed as -m on the documentation). However chaning the -m flag to -S, I get a different error:

...
Reading input tree file ethiopia_36min_parti.nex.best_model.nex.treefile ...ERROR: File not found or incorrect input, pls check it again. (line 2 column 0)

I even tried the different model files generated by IQTree2 with variations of the -m and -S flags. So I do not believe that -m to -S is the solution.

However, I know these files I am using should work because I have run them using --scf which warns me I should use --scfl flag when completing the analyses. In both cases using -m and -S flags work fine for the --scf flag. Lastly, I further tried changing my input tree flag from -te to -t which produces the same errors I've described previously when testing -t with the -m and -S flags.

Here are the associated input files for my smallest dataset example_scf_error.zip. Within it are example_scf successful runs and the example --scfl error log. Please ignore the quality of the input data, it is fairly "raw" and unprocessed for some issues I have resolved in a parallel dataset.

[bqminh]

Sorry for the delay. This is because ethiopia_36min_parti.nex.best_model.nex is a partition file and should be used as such input, see for example http://www.iqtree.org/doc/Advanced-Tutorial#partitioned-analysis-for-multi-gene-alignments. -m is for specifying single models, not partition models.