bootstrap analysis did not converge. You should rerun with higher number of iterations (-nm option)

[Max_IT]

Hi, I have just run the following script:

iqtree -st DNA -s ../myalignment.varsites.phy \
    -m GTR+F+ASC+R5 -nt AUTO -ntmax 10 -pre ww.13k.reduced.iteration2 -alrt 1000 -nm 5000 -lbp 1000 -bb 1000 -bnni

In the log file I found the warning:

bootstrap analysis did not converge. You should rerun with higher number of iterations (-nm option)

I increased the -nm to 5000, but the warning remains. i just wanted to make sure if the script is correct, or if the -nm 5000 should replace the number of replicates (1000).

Thank you for your kind attention,

Max

[Minh Bui]

Hi Max,

Your command line looks fine. -nm 5000 will set the max number of iterations to 5000. This warning means that it’s a difficult dataset, e.g. with low phylogenetic information. How many sites does this alignment have? If not long, look at previous discussions about short alignments. Unfortunately I don’t have access to Google group etc. now to find out the forum topic, as I’m currently in China and thus behind the Great Firewall.

Cheers,

Minh

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[Max_IT]

Hi, Minh,

Thank you for your kind answer. The alignment is 13K sites long; I had previously checked the signal with DAMBE and it was fine; I later removed a few sequences though, I will check the signal again.

Thank you for your kind help,

Max

[Minh Bui]

Hi Max,

I just found the issue, that with -bnni option, this warning is not correct. So please ignore it!

Thanks,

Minh

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