no mcmc parameter .log file

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Aurélien DE JODE

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Nov 28, 2025, 5:32:29 AM (yesterday) Nov 28

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Hello,

This is my first time running mcmctree.
I am using mcmctree iqtree version (MCMCTREE in paml version 4.10.8.iq2mc, November 2024).
I followed the iqtree3 tutorial to produce the hessian file (https://iqtree.github.io/doc/Dating)
Then I am running mcmctree on a slurm cluster using the attached script and .ctl file.

I do not get and .log file despite specifying it in the .ctl file.
Is that an expected behavior ? If yes then I guess the MCMC log of parameters to examine in Tracer is to be found somewhere else ?

Thanks for your help with this.

Sandra AC

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Nov 28, 2025, 5:36:39 AM (yesterday) Nov 28

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Hi there,

Thanks for your message! It looks like this issue is more related to IQ-TREE3 than to PAML -- the version you are using is not developed nor maintained by PAML. You may have to reach out to the developers (e.g., post an issue on their GitHub site) to figure out what the problem might be if related to the software -- perhaps it could also be related to how you have submitted the job to the server, but that is something the research software engineers at your institution could help you with as every server has specific requirements.