UFBoot does not converge even with 5000 `nmax`

[Liu Jia]

Hello,

I am using the IQTREE version 2.2.0 to construct phylogenetic trees for the alignment of 1200+ genes, and got the convergence issue (even with 5000 iterations and 0.2 perturbation) as shown below:
"""
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.925
NOTE: UFBoot does not converge, continue at least 100 more iterations
"""

My command looks like this:
`iqtree2 -s ../0.95_rogues_removed_msa.fa -m TVM+F+R10 -pers 0.2 -nstop 500 -B 1000 --abayes --alrt 1000 -T AUTO -ntmax 15 --nmax 5000 --boot-trees --prefix iqtree2-nmax-5000-pers-0.2-rep1_0.95_rogues_removed_msa_result`


Here are more information about my sequence alignment:
"""
WARNING: 6 sites contain only gaps or ambiguous characters.
Alignment has 1252 sequences with 1231 columns, 920 distinct patterns
777 parsimony-informative, 117 singleton sites, 337 constant sites
"""

I created 10 trees all with 5000 iterations, perturbations from 0.1 to 0.5 (with increment at 0.1), two replicates at each perturbation. And they all failed to converge. Is there anything you would recommend for the next step to try out? Does adding `-bnni` to my commands help? If with `-bnni` the trees still do not converge, can I ignore the convergence warning with IQTREE v2.2.0?

Thanks,
Jia

[Omar Idris]

I got suggestions to increase and indeed adding one more iteration to 1001 UF. 

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ONI