Error with parameter mu (BEAST 1.10.0)

[Kévin Jean Louis Maurin]

Hi everyone,

I am trying to run an analysis using default parameters, just to have a go with a small dataset (4 chloroplast genes for 46 taxa). I am using BEAUti/BEAST 1.10.0, HKY model, strict clock, Yule process, on Ubuntu.

When I run the XML file in BEAST, the run stops after a few paragraphs and the terminal window closes before I can see what happened. My supervisor ran the XML on Windows and he could retrieve the error message:

"SEVERE: Parsing error - poorly formed BEAST file, Concatenated_alignments_accD_matK_ndhF_rbcL_realigned.xml:

Error parsing '<statistic>' element with id, 'mu':

Unknown statistic name, mu"

Why is mu of the kappa prior not recognised by BEAST? What do you you think I should try to make it work?

I also tried to run it again by ticking the "Mean/Stdev in real space" box of the kappa prior settings, so that "mu" was changed for "mean", but still the run crashes.

Thank you in advance for your help!

Cheers,

Kévin

[吕小祜]

We are at a loss and puzzled as follow:

在 2018年11月23日星期五 UTC+8下午2:45:12，Kévin Jean Louis Maurin写道：

[Guy Baele]

Hi Kévin,

Can you first try to set up your analysis again with BEAUti 1.10.4 and then run it with BEAST 1.10.4 ?
You can find those versions here: https://github.com/beast-dev/beast-mcmc/releases

Please let us know if the problem persists.

Best regards,
Guy

Op vrijdag 23 november 2018 07:45:12 UTC+1 schreef Kévin Jean Louis Maurin:

[Kévin Jean Louis Maurin]

Hi Guy,

Thank you for your reply. I tried on Ubuntu and once again it crashed without giving me a log file, so I ran it on Windows and got a different error message:

"Using BEAGLE DataLikelihood Delegate

BEAST has terminated with an error. Please select QUIT from the menu.

Failed to load BEAGLE library: no hmsbeagle32 in java.library.path

Fatal exception: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements.

java.lang.RuntimeException: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements."

So, I I will try installing the BEAGLE library, and will keep you posted on my progress.

Cheers,

Kévin

[Kévin Jean Louis Maurin]

Hi again,

I installed BEAGLE and the latest version available for Windows is a 64-bit version.

I followed the instructions of the developer to install BEAGLE (I just had to restart the PC after installation), then tried running my XML again, and I got the same error message as before. It seems like BEAST is trying to find a 32-bit version of BEAGLE (the error message mentions "no hmsbeagle32 in java.library.path").

So, how can I make BEAST understand that the version I have is a 64-bit, not 32?

Cheers,

Kévin

[Andrew Rambaut]

I think it may be the Java version that is 32-bit. Try reinstalling Java.

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK

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[Andrew Rambaut]

I think it may be the Java version that is 32-bit. Try reinstalling Java.

Andrew

On 25 Nov 2018, at 21:26, Kévin Jean Louis Maurin <kj...@students.waikato.ac.nz> wrote:

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[Kévin Jean Louis Maurin]

Hi Andrew,

I now have installed Java for 64-bit, BEAGLE for 64-bit and BEAST v1.10.4, but when I start BEAST I still have the error message "Failed to load BEAGLE library: no hmsbeagle64 in java.library.path" and "BEAGLE not installed/found".

Do I need to tell BEAST where to find the library? Or to move the installed files of BEAGLE into the BEAST folder?

Cheers,

Kévin

[Andrew Rambaut]

So it looks like it is now trying to find the 64-bit version of BEAGLE which is good. I suggest now you remove all the files for BEAGLE that you can find (I am not familiar with Windows and where it store things but I assume a search will find these). Then reinstall BEAGLE with the installer.

If that doesn’t work then I am going to have to defer to a Windows expert.

Andrew

[Kevin Jean Louis Maurin]

Hi Andrew,

I just fell by accident on the "Java" page of the BEAST documentation website and it appears that I installed the Java browser plugin, not JRE. So, I installed JRE on Windows and now everything is working fine!

I tried the same thing on Ubuntu but BEAST is still unable to find the BEAGLE library (after carefully following the installation process for the library I still got an error message so I am not even sure that the library was installed correctly...). I'm tired of fighting for the moment so I'll go with Windows.

Thank you for your help :)

Cheers,

Kévin

--

Kévin Maurin

PhD student in Botany and Molecular Phylogenetics

The University of Waikato - Te Whare Wānanga o Waikato

kj...@students.waikato.ac.nz | +64 (0)22 460 2262

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[Alejandra Panzera]

Hello,

I have a similar error trying to run a very simple data set with 10 loci and 56 terminals:

dr.xml.XMLParseException: Error parsing '<statistic>' element with id, 'mu':

Unknown statistic name, mu

Valid statistics are:

at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

Mar 27, 2019 3:26:21 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, TEST.xml:

Error parsing '<statistic>' element with id, 'mu':

Unknown statistic name, mu

I get the error on MAC using beast 1.8.4, and in CIPRES using the same version of beast. With version 1.10.4 I get this error:

Mar 28, 2019 11:09:15 AM dr.app.beast.BeastMain <init> SEVERE: Error running file: infile.xml Mar 28, 2019 11:09:15 AM dr.app.beast.BeastMain <init> SEVERE: Parsing error - poorly formed XML (possibly not an XML file): Premature end of file. srun: error: comet-02-15: task 0: Exited with exit code 1

I hope you can help me out! Thanks in advance,

Alejandra