MCMCtree stepping-stone error

[­임원섭 / 학생 / 지구과학교육과]

Hi, am trying to run a stepping stone analysis for clock model selection in MCMCtree (PAML v 4.10.7). I followed this tutorial: https://dosreislab.github.io/2017/10/24/marginal-likelihood-mcmc3r.html and generated 32 ctl files corresponding to each beta points. However, when try to run the analysis, after few minutes this error message shows up:

What could be the problem? I will willingly provide setup files if needed. Thanks in advance!

[­임원섭 / 학생 / 지구과학교육과]

Just found that I can directly upload files in this group. I'm appending sequence, tree and control files. Thanks!

2024년 6월 29일 토요일 오전 2시 15분 2초 UTC+9에 ­임원섭 / 학생 / 지구과학교육과님이 작성:

[Sandra AC]

Hi there,

Thanks for your message! I have tried to reproduce the error but have not been able to -- MCMCtree runs without problems when using PAML v4.10.7. Which PAML version are you using? Also, make sure that the alignment is correct as it seems you have a lot of empty sequences.

All the best,
S.

P.S.: I guess that you just included the input files for the first beta point, but make sure that you run MCMCtree for the rest of the beta points as the tutorial specifies too!

[­임원섭 / 학생 / 지구과학교육과]

Hi, thank you for your response! As you mentioned, re-running the command did not result in any problems (I am using PAML v 4.10.7 just as you did). I have no clue why I had that error message in the first run. (Probably has something to do with the random seed?)

Thanks and have a good day!

2024년 6월 29일 토요일 오후 7시 43분 34초 UTC+9에 sandr...@gmail.com님이 작성: