Hi @mbosmeny! You are correct that not all internal steps of IQ-TREE’s tree inference can be parallelized, so there will be times when IQ-TREE only uses a single core.
One way to check what is happening behind the scenes is to inspect the IQ-TREE log. In our “ncov” workflow, this file is written out to your build’s results directory (e.g., results/test/) with an extension of .iqtree.log. This file contains a report of how many cores IQ-TREE thinks it has and how much time it spends on each step of the inference. You may also try running IQ-TREE manually with -nt AUTO and inspecting the beginning of the log output. In this mode, IQ-TREE will try to determine the optimal number of cores to use for tree building. If you see unexpected output from this command, that may help you track down the issue.