BUG: Issue with loci.treefile between PC and Mac

[Ewald J.Z. Groenewald]

Good day,

I have an issue with running the concordance testing on my Mac. I follow the instructions given in Chapter 7 of the manual and all files are generated. However, the loci.treefile only contains a single tree. When I use the same input files (alignment and partition file) on a PC, and I run the IQ-TREE analysis using the same command line, the loci.treefile contains the individual gene trees. I have tested this on both a Mac laptop running OS 10.14.6 and a Mac Pro running 11.5.1, so the issue seems not to be related to the Mac OS?

I paste below the command line used, and the lines from the log file.

Any ideas would be appreciated!

All the best,

Ewald

bin/iqtree2 -s XXXXXXXX.nexus -p XXXXXX_partitions.nex --prefix loci -T 2

Q-TREE multicore version 2.1.3 COVID-edition for Mac OS X 64-bit built Apr 20 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    xxxxx.local (AVX512, FMA3, 48 GB RAM)
Command: bin/iqtree2 -s CScitricolaTrincinctumTEFRPB21RPB22RPB1CAL.nexus -p CScitricolaTrincinctum_partitions.nex --prefix loci -T 2
Seed:    794288 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Aug 10 09:31:43 2021
Kernel:  AVX+FMA - 2 threads (32 CPU cores detected)

otal number of iterations: 103
CPU time used for tree search: 38.503 sec (0h:0m:38s)
Wall-clock time used for tree search: 19.389 sec (0h:0m:19s)
Total CPU time used: 38.753 sec (0h:0m:38s)
Total wall-clock time used: 19.500 sec (0h:0m:19s)

Analysis results written to:
  IQ-TREE report:                loci.iqtree
  Maximum-likelihood tree:       loci.treefile
  Likelihood distances:          loci.mldist
  Screen log file:               loci.log

Date and Time: Tue Aug 10 09:32:10 2021

[Minh Bui]

Hi Ewald,

This is because you used -p option, which constructs a single concanetation tree.

What you want is -S option instead of -p. That will infer individual trees for each locus.

Cheers

Minh

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