iq-tree getting stuck using PMSF approximation and -bnni

[Matias Wanntorp]

Hello,

I have been trying to run iqtree with LG+C60+G+F with PMSF -bb 1000 -bnni however it gets stuck and the last thing printed to the log for 15 hours is: "Refining ufboot trees with NNI 1 branch..."

Together with the model. Is there a bug related to this?

Here is the beginning of my log: 

IQ-TREE multicore version 2.2.2.6 COVID-edition for Linux 64-bit built May 27 2023

Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,

Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    r30.uppmax.uu.se (AVX2, FMA3, 251 GB RAM)

Command: iqtree2 -s bigtree.Apr.5.2024.fasta -m LG+C60+G+F -ft ../../guide_tree_Apr.5.2024/bigtree.Apr.5.2024.fasta.iqtree.treefile -st AA -nt 20

 -mwopt -bb 1000 -bnni

Seed:    878910 (Using SPRNG - Scalable Parallel Random Number Generator)

Time:    Sat Apr  6 02:47:55 2024

Kernel:  AVX+FMA - 20 threads (20 CPU cores detected)

Reading alignment file bigtree.Apr.5.2024.fasta ... Phylip format detected

Alignment most likely contains protein sequences

Constructing alignment: done in 0.422406 secs using 746.6% CPU

Alignment has 80 sequences with 86500 columns, 82538 distinct patterns

65433 parsimony-informative, 8108 singleton sites, 12958 constant sites