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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
GNU General Public License v3.0
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Mcmctree not running when using a Mac M1 silicon #45

Open DoveOfGlass opened 8 months ago

DoveOfGlass commented 8 months ago

Hello everyone! :)

I just installed PAML in my Mac (Mac mini (M1, 2020)). Baseml and others work, but mcmctree gives me an error related to hardware incompatibility: "zsh: illegal hardware instruction /Users/palomaruizdd/paml/bin/mcmctree", after reading the tree correctly.

I have tried using Roseta 2 (and I have checked the path and the permits, they are fine), and I have compiled and tried two different versions of PAML (4.8 and 4.10), but the error persists. Any clues? Is there any compatible version of mcmctree with Mac M1?

I have used it previously installing it with miniconda, but it does not seem to be available anymore.

Thank you for all the help!! Paloma

sabifo4 commented 8 months ago

Hi there,

Thanks for reporting this problem! You may need to download the dev branch of the PAML GitHub repository and recompile the programs if the currently executable files are not compatible with your Mac M1. You can follow the next steps:

  1. Change to the dev branch in the main GitHub repository (by default, you should see the branch is main).
  2. Press the green button with the word Code , then you should see that a zip file called paml-dev.zip starts being downloaded.
  3. From then onwards, you can follow the same instructions given in the installation procedures for UNIX/Linux in the PAML Wiki, which will compile all PAML programs.
  4. Once you have the new MCMCtree executable file, give it executable permissions and try to run a test analysis with this binary.

Please let us know if this approach works so that we can close this issue or suggest other alternatives :)

All the best, S.

sabifo4 commented 7 months ago

I will now close this issue as I assume everything worked and the user forgot to post a reply here. If there are further issues, please reopen :)

DoveOfGlass commented 4 months ago

Hi everyone!!! :)

Sorry for the (super) late response! I had not have access to my computer in a long time. Thank you very very much S for the help :)

I tried what you suggested, and yes, compiling the paml-dev worked in my Mac M1.

Baseml worked straight away. I had a little bit problem with mcmctree (Mac is very picky sometimes XD). The classic: mcmctree was not finding baseml.

Just in case there are more Mac users having the same problem: what worked for me was exporting the path for paml-dev and BASEML to my .bashprofile, applying the changes and running mcmctree from the main user. Now everything is running smoothly!

I hope that this is helpful for anyone :)))

All the best! Paloma