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kfuku52 / RADTE

Divergence time estimation in the complex history of gene family evolution
MIT License
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Error for gene tree processing #5

Closed zbyxinalice03 closed 2 years ago

zbyxinalice03 commented 2 years ago

Hi everyone: I try to run the RADTE program using my dataset. I replaced "_" into "." in gene id, and modified species name into "genus_speicies". Then I executed Notung-2.9.1.5 to produce the rooted gene tree, with "--resolve" model used to avoid the polytomies. My issue is that there is an error after "calibration node removed" when I ran RADTE, showing that "All attempts for divergence time estimation were failed. Exiting":

error1 I can't figure out the reason for this error，have anyone met this error before?

kfuku52 commented 2 years ago

Bifurcation should be done before running NOTUNG, and the task command of NOTUNG should be --reconcile rather than --resolve to make it compatible with RADTE. Could you try that?

zbyxinalice03 commented 2 years ago

I will try to perform bifurcation. Is there any program you recommand to do this?

kfuku52 commented 2 years ago

I used to use ape's multi2di.

zbyxinalice03 commented 2 years ago

OK, I'll try it. Thank you very much.

zbyxinalice03 commented 2 years ago

Hi: My colleague recently found that there is an spelling error in your "README.md" file. In the part of "Example 1: RADTE after NOTUNG", "--chronos_model=difscrete" should be "--chronos_model=discrete". When my colleague modified this parameter, the program could be executed. We will try to perform the program using our own data after.

kfuku52 commented 2 years ago

Thank you for reporting it. I will correct the typo.