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abacus-gene / paml

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli
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‘Error: strange calibration?.’ when second ronud of mcmctree #29

Closed yanyew closed 1 year ago

yanyew commented 1 year ago

I used a tree file with calibration for first round of mcmctree, and generated out.BV. But when I use the out.BV as in.BV and the same tree file for the second round 0f mcmctree, it failed and reported ‘Error: strange calibration?.’

The tree file is: 30 1 (((Dre,Cau),((Ots,Omy),((Oni,(Pny,Nbr)'B(14.1,30.1)'),(Osi,Ola)))),((Cpi,Gga),(((Ptr,Hsa),(((Fca,(Pti,Ple)'B(11.6,14.7)'),((Clud,(Cluf,Clufgsd)),Vvu)),((Cwa,Ssc),((Bta,(Bmu,Bgr)),(Chi,Oar))))),(Mau,(Mmu,Mca)))));

sabifo4 commented 1 year ago

Hi there,

Actually, there are many things that could have gone wrong here. With only a tree file with calibrations, however, it is quite hard to find out whether the issue is in the input files, the settings in the control file, your working environment, etc. Please note that, when you report a problem, you need to make sure that you provide the software developer/s with all the information and files that are required to reproduce the error you are getting (e.g., input files, control files, other settings you defined to run the software, etc.) so they can debug the code accordingly.

Also, please note that this type of queries are to be reported in the PAML discussion group.

I am closing this issue as there are no problems with regards to the code in MCMCtree. In addition, I do not have enough information to further troubleshoot what may have gone wrong in this analysis. Please post further questions in the PAML discussion group aforementioned and attach any files that are required to reproduce the error you are getting.

Thanks!