"Error: implement SkewN, Skewt, S2N now."

[R.M.D...@salford.ac.uk]

I'm getting an error with MCMCTree that I hope you can help me with! I am running paml4.10.7 on a Windows machine, via Windows Power Shell with Ubuntu. I have been trying to run an analysis with a mix of bound (B) and Skew-T (ST) calibrations, but the Skew-T calibrations seem to be causing problems. An analysis with only bound calibrations runs  correctly, but when I include one or more Skew-T calibrations, I get the following error message:

Fossil calibration information used.
Node  73:  ST (  0.1340,  0.0090, 50.0000,  1.0000 )
4576 bytes for rates.

Reading branch lengths, Gradient & Hessian from in.BV.
Locus 4: 72 species
150000 burnin, sampled every 400, 20000 samples
Approximating posterior
(Settings: cleandata=1  print=1  saveconP=0)

getting initial values to start MCMC.

Error: implement SkewN, Skewt, S2N now.

I thought it might be because some of the Skew-T calibrations might be incompatible, but I still have the error when only a single Skew-T calibration (and no bound calibrations) is present, at the root - I am attaching this version here. The analysis runs fine on an earlier version of MCMCTree (paml 4-10.5). 

Do you have any advice here?!

Thanks,

Robin

[Sandra AC]

Hi Robin,

Thanks for your message! Unfortunately, I have not been able to reproduce your analysis. I have run PAML v4.10.7 (Windows Subsystem for Linux, Ubuntu) with your input files and I have managed to complete my test run -- I also decreases `burnin`, `sampfreq` and `nsample` as I wanted to run a quick test. Please find the "out.txt" file I have obtained attached. Are you using the latest stable release of PAML? Note that you should see the following on the screen output as the first line: "MCMCTREE in paml version 4.10.7, June 2023".

Please let us know if you are using the latest stable release and, if so, whether you have been able to run the program using the ST distribution as a root age constraint.

All the best,
Sandy

P.S.: Are you using the Windows Power Shell or the Windows Subsystem for Linux?

[R.M.D...@salford.ac.uk]

Hi Sandy,

Thank you for your very quick and helpful reply! Yes, I am using the latest stable release (4.10.7). I get the same error message with Windows Power Shell, and Windows Subsystem for Linux. I will keep investigating. paml 4.10.5 seems to work fine - do you know if there are there any major differences between the two versions that mean that I should use 4.10.7?

Thanks again for your help!

Robin

[Sandra AC]

Hi Robin,

I am not sure what the problem is as I do not know which binaries you are using to run MCMCtree, but I believe it is not the latest stable release as I cannot reproduce your error (I have tried again with both the pre-compiled binaries from the PAML GitHub repository, Linux and Windows).

You can download the Linux pre-compiled binaries from the PAML GitHub repository...



... then decompress the files and save them on your preferred location. Firstly, go to bin and you shall find there the PAML programs. To test your files and make sure they work, you can do the following:

- Copy your input alignment and tree files, the control file, and the "in.BV" file inside the bin directory -- E.g., create a new directory called test.
- Open a terminal in the "bin" directory and give executable permissions to the binaries (chmod 775 *)

- Copy the mcmctree binary inside the test directoy.

- Using the terminal, change directories to test, and then run MCMCtree by typing ./mcmctree mcmctree.ctl

This is what I did on my PC using the WSL and MCMCtree runs without problems while using ST distributions as node age constraints.

I have also tested the Windows executable (download link from the PAML GitHub repository) using the Windows Power Shell. Remember that Linux commands such as "cd" will not work, you need to use the Windows language. You can do the same test as above (remember to use the Set-Location command to change directories from the Terminal) and run MCMCtree by typing  .\mcmctree.exe mcmctree.ctl

There have been some changes since PAML v4.10.7, and so it is always best to use the latest stable release when available -- you can check the changes from version to cersion via this link!

Hope that now things run, please let us know :)

All the best,
Sandy

P.S.: I cannot attach executable files, hence why I have explained how you can download them from the PAML GitHub repository and run the tests on your PC with your input files, hope that this is fine!