MCMCtree not giving MCMC log output file

[­임원섭]

Hi, 

I am using the IQ2MC pipeline to date a phylogenetic tree. I successfully created in.BV file using IQtree3 and ran the .ctl file with PAML v 4.10.9. The job launched well, but even after the job was done, no MCMC log files were written to the directory. Can anyone help me with this? I am appending a complete set of files needed to run the analysis.

Best, Wonseop

[Sishuo Wang]

Hi Wonseop,

Thanks for your question! I think the burnin is simply too big. btw, you might wanna use the may 21 version or its later version for iq2mc (see also https://github.com/iqtree/iqtree3/issues/70, https://github.com/iqtree/iqtree3/issues/69).

best,

sishuo

[­임원섭]

Hi Sishuo,

Well, adjusting a burn-in & using the iq2mc version of paml worked in most cases. However, when using the nucleotide mixture model to calculate gradients and Hessians, the job keeps terminating without any log files (.log), even when using the same settings as the other analyses that worked well (edge-linked partitioned model and amino acid mixture model in my case). I appended the compressed folder with the files needed to run the analysis. I'd appreciate it if you could have a look.

Thanks in advance!

Best, Wonseop

2025년 7월 14일 월요일 오후 6시 2분 34초 UTC-7에 Sishuo Wang님이 작성:

[Sishuo Wang]

Hi Wonseop,

I see. It could be not so easy to tell what happens. i would suggest you ask the question at iqtree3 github and there would be experts helping you. If you are working on aa (mixture) model, you can also try phylohessian and if it doesn't work pls don't hesitate to let me know. Alt, an easier way is to use the bootstrap approach bs_inBV which in general gives you a good approx to the hessian that is needed for mcmctree's approx lik dating method.

best,

sishuo

[­임원섭]

Oops,

Sorry Shishuo. I just realized that I was using an older version of IQTREE for the calculation. Using v 3.0.1 solved the problem. Thanks for the help!

2025년 8월 1일 금요일 오전 1시 13분 16초 UTC-7에 Sishuo Wang님이 작성: