Beauti 2 file production issues - can't save .xml files

[HKen]

Hello,

I am new to BEAST and this forum, so I apologize if this is a simple or redundant question, however I haven't found any other postings that quite answer my question.

I am finding that when preparing a file in Beauti 2, only sometimes do the changes I make actually save into my .xml file. Often I make changes and try to save them but they are not reflected in the .xml file. I also cannot save as a new file. It seems that this is happening after I constrain a number of clades to be monophyletic, but I don't know if this is related. I would really appreciate any suggestions of what might be happening here.

I've attached my nexus file and the most complete version of the .xml file that I have been able to generate so far.

Thanks in advance for any advice,

Haley

[Remco Bouckaert]

Hello Haley,

I had a look at your file and it loads fine in BEAUti, and I can save the file after adding constraints Given that saving is not possible, nor does 'save as' works, there may be something going wrong when BEAUti  is preparing for the model to be saved. Perhaps there is some interference with a BEAUti template from some package, if you installed any packages.

One way to get more information is to run BEAUti from the command line (see http://blog.beast2.org/2014/03/18/on-the-bleeding-edge-with-beast-2-using-dev-build-from-command-line-and-running-beast-faster-on-windows/ for details). Whenever you try to save, messages on the command line should give a better indication on what goes wrong. Let me know if this happens again.

Cheers,

Remco

PS Do you have the latest version (currently 2.1.3) installed?

[Simey]

I m experiencing something similar. I cannot save .xml files from Beauti 2.4. The file is never written and there are no error messages. I will try launching beauti from the command line, but I have created large taxon sets (hundreds of individuals) and would rather not do that again if possible.

[Remco Bouckaert]

There was an issue with v2.4.0 that caused this file saving problem with some taxon names. This is resolved in v2.4.1, so if you could upgrade to the latest version and try again. Let me know if there is still a problem with saving from BEAUti.

Cheers,

Remco

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[Simey]

2.4.1 resolved this. thank you.

[Guangpeng Ren]

Sorry, I found it. Thank you!

Guangpeng

[Guangpeng Ren]

Dear Remco,

I also have the same problem with BEAST2.4.0. I would like to upgrade to the latest version, but could not find where to download. Could you please let me know where i can download it? I am using MAC. 

Cheers,

Guangpeng

On Saturday, April 30, 2016 at 12:30:00 AM UTC+2, Remco Bouckaert wrote:

[EvoClive]

Seems to be happening on 2.4.7 also

Clive

[EvoClive]

And 2.4.8

[André Elias Rodrigues Soares]

I guess I'm not alone… Still happening on 2.5.2.

[Remco Bouckaert]

Hi All,

I am not sure why this happens, but what may be able to diagnose the problem is when this happens, to have a look at the menu "Help/Messages” in BEAUti and post the information in the dialog? 

Thanks,

Remco

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[Walter Xie]

Hi everyone,

I just tested Haley's XML in BEAUit 2.5.2, and I had no problem to save my changes in both clock model and tree prior. The changed XML is attached.

Can you please always use the latest released version? If you still have the same problem, please give us some details of the process and your system. In addition, as Remco suggested, the message from the menu "Help/Messages” would be very helpful to identify the problem.

For example, I used Mac OS 10.14 and Java 10. I loaded the XML into BEAUti 2.5.2, and changed the Yule to Coalescent Constant, and changed Relaxed clock to Strict clock, and then saved the file. 

Cheers,

Walter