MCMCTREE error nfossil

[Emmanuelle Morin]

Hello,

I'm new to PAML and I try to use MCMCTREE to estimate species divergence times. I'm working with protein alignment so I'm doing these different steps:

mcmctree mcmctree.ctl

codeml tmp0001.ctl

mcmctree mcmctree.ctl

At the third step I have this error : 

priors: 

mu_i ~ gammaDir(2.000, 20.000, 1.000), SD(mu_i) =  0.07071, corr(mu_i,mu_j) = -0.50000

sigma2 ~ gammaDir(1.0000, 10.0000, 1.0000)

Error: nfossil....

I can't find any lead on the FAQ concerning this error, could you help me here ?

Thanks,

Emmanuelle

[cpo...@oakland.edu]

I am also getting the same error after running a similar analysis. Emmanuelle, would you happen to be running your analysis on Unix / Linux? I have tested my setup on both Windows and Linux (CentOS) and Linux is giving me the error, not windows. Hopefully we can get a fix for this! I also cannot find anything that mentions the nfossil error.

Cheers,

Chris 

[Emmanuelle Morin]

Hi,

I'm running it on Scientific Linux. Do you mean that on Windows you get a result ?

Cheers,

Emmanuelle

[Christopher Powell]

Correct! I was able to get a result for a test run on Windows. I tested this to see if it was a platform difference and maybe that is the problem. It seems as if Scientific Linux is based off of Red Hat and CentOS is quite similar. Maybe it is a Red Hat problem.

Cheers,

Chirs

[Ziheng]

if you send me a copy of the files, i can try to take a look.  i hope the dataset is small.

best,

ziheng

[Christopher Powell]

Hello Ziheng,

I decided to search the source code of mcmctree for the error I was getting. After digging for a while, I found where it was printing the error, line 2467 - 2468. I then opened an older version of mcmctree to compare and these two lines did not exist in the other version I looked at. Simply commenting them out allowed for the program to run without any problems while also giving results that looked correct (had older runs to compare it too). This is clearly not an official fix. Does this break mcmctree to remove this small if statement?

 if (nfossil != stree.nfossil)

      error2("nfossil...");

Thanks,

Chris

[npbha...@gmail.com]

I am running paml v4.9 and running into the same error with the example data in the program. 

Error: nfossil....

[Ziheng]

do the different versions behave differently.  

i checked doc/pamlHistory.txt, and there is one entry as follows.  you can get the most recent version at the web site.  ziheng

Version 4.9e, March 2017

(*) mcmctree.  A bug was introduced in version 4.9b which causes the

program to read the fossil calibration information in the tree file

incorrectly, if joint (minimum and maximum) bounds are specified using

the symbol '<' and '>'.  If you use the notation "B()", "L()", and

'U()', the information is read correctly.  This bug was introduced in

version 4.9b and exists in 4.9c and 4.9d.  Versions 4.9a and earlier

were correct.