Error: maintree file can have only one tree.

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Kelly

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Oct 11, 2023, 9:08:10 AM10/11/23
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Any help with this error? My tree file does in fact have only one tree in it.

Sandra AC

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Oct 11, 2023, 9:17:18 AM10/11/23
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Hi Kelly,

Can you please share the tree file and the control file you are using? In that way, it will be easier for troubleshooting :) 

Cheers,
S.

Kelly

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Oct 11, 2023, 9:38:47 AM10/11/23
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Whoops, I think I sent that as a PM by accident. Let me know if you didn't get it, Sandra. And thank you again for the help!
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Skip

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Feb 5, 2024, 2:20:31 PMFeb 5
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Was there a solution to this problem? I'm having the same issue. Attached are my tree and control file.
gecko_mcmctree.ctl
gecko_inTree.tre

Sandra AC

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Feb 5, 2024, 2:36:02 PMFeb 5
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Hi there,

I am not sure I received Kelly's private message nor a notification with the latest message in October, sorry! Kelly, if you are still following this thread of messages and still need help, please send your files so that I can check again.

Skip, your tree file has branch lengths and the notation that you are using for the calibrations is incorrect (i.e., wrong format). In a nutshell, you have soft-bound calibrations following this format: "B-2.356-2.631-9.99999999999999e-301-0.025-". You should follow the format "B(min_age,max_age,min_tail,max_tail)". For hard bounds, please use "1E-300" -- not sure what "9.99999999999999e-301" is supposed to mean. I have seen that you also have lower bounds, which also follow the wrong format. You can find all the details regarding the PAML notation to incorporate node age constraints in the PAML documentation (pp. 49-52). As aforementioned, please also remove the branch lengths as detailed in the PAML Wiki too. Seeing that you have formatting issues in your input files, please check that your input sequence file is correctly formatted -- you will also find all this information in the PAML Wiki.

Hope this helps!
S.

Skip

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Feb 5, 2024, 3:36:18 PMFeb 5
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Thank you. I've been using the R package MCMCtreeR since this is such large and unwieldy tree. I thought that the calibrations looked funky, but I was hoping PAML wouldn't get bogged down by that. I'll give this another try.

Thanks again.
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