Opening xml in BEAUti takes too long

[Špela Borko]

Hi,

I have a sequence dataset of 180 taxa, 6100 characters, 9 partitions, and BEAST 2.5.0. When I load nex file into BEAUTI and save it as xml, I can reopen it. However, if I set site and clock models, save and try to reopen, nothing happens. No error, it seems that the program is processing but is never finished. I tried to increase memory usage - nothing. I saw similar issue in one other thread, but their file was way larger than mine.

I have minimal computer knowledge, and I am only starting to learn BEAST2 so I would appreciate any help.

I use computer with cpu intelcore i7-7500u, gpu nvidia geforce 930mx 2gb, 16gb ram, 256gb ssd+1tb hdd and os Windows10.

Thank you for your help!

Špela.

[Remco Bouckaert]

Hi Špela,

Possibly, BEAUti crashed for some reason. Can you open the menu Help/Messages and post the content of the dialog?

Cheers,

Remco

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[Špela Borko]

Hi Remco,

I tried for few times but it freezes completely. I have to shut it down through task manager. Or sometimes I get a message: "Error and warning messages are printed to Stdout and Stderr To show them here, start BEAUti with the -capture argument." When I managed to get to Messages, among other things there was also OutOfMemoryError, but unfortunately I did not copied it. 

I did not find the answer how to increase memory usage for beauti on windows, can you help me with that maybe? Or tell me that I am thinking into completely wrong direction an I should do something else :).

I also tried to delete everything, download and unzip files again, no difference.

 I am pasting messages that appear when I launch beauti:

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

Warning: corrupt classpath entry: 

Warning: corrupt classpath entry: 

Loading template D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\templates\Standard.xml

Investigating 

Investigating C:/Users/SpelaB/BEAST/2.5/BEAST

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\ClockModels.xml

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\ParametricDistributions.xml

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\Standard.xml

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\StarBeast.xml

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\SubstModels.xml

Processing C:\Users\SpelaB\BEAST\2.5\BEAST\templates\TreePriors.xml

Investigating .

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\ClockModels.xml since ClockModels.xml is already processed

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\ParametricDistributions.xml since ParametricDistributions.xml is already processed

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\Standard.xml since Standard.xml is already processed

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\StarBeast.xml since StarBeast.xml is already processed

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\SubstModels.xml since SubstModels.xml is already processed

Skipping D:\phylo_programi\BEAST.v2.5.0.Windows\BEAST\.\templates\TreePriors.xml since TreePriors.xml is already processed

connect => beast.app.beauti.BeautiConnector

subtemplate => beast.app.beauti.BeautiSubTemplate

Uniform => beast.math.distributions.Uniform

Normal => beast.math.distributions.Normal

OneOnX => beast.math.distributions.OneOnX

LogNormal => beast.math.distributions.LogNormalDistributionModel

Exponential => beast.math.distributions.Exponential

Gamma => beast.math.distributions.Gamma

Beta => beast.math.distributions.Beta

LaplaceDistribution => beast.math.distributions.LaplaceDistribution

InverseGamma => beast.math.distributions.InverseGamma

prior => beast.math.distributions.Prior

map

map

map

map

map

map

map

map

map

map

map

map

beauticonfig

fragment

run

===============================================================================

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA,

  Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian

  evolutionary analysis. PLoS Computational Biology 10(4): e1003537

===============================================================================

Warning: at least one operator required to run the MCMC properly, but none found.

template item TreeOperators is ignored

PARTITIONS0:

[[], [], []]

InPosterior=posterior prior likelihood 

Could not find beastObject with id treeLikelihood.Species. Typo in template perhaps?

Validation message: At least one input of name 'xx' must be specified.

Validation message: At least one input of name 'xx' must be specified.

Validation message: At least one input of name 'xx' must be specified.

Validation message: At least one input of name 'xx' must be specified.

class beast.core.MCMC != class beast.core.Runnable

PARTITIONS0:

[[], [], []]

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

BeastMain found in C:\Users\SpelaB\BEAST\2.5\BEAST\lib\beast.jar

Thank you and have a nice day,

Špela

Dne sreda, 30. maj 2018 21.42.40 UTC+2 je oseba Remco Bouckaert napisala:

[Špela Borko]

Update:

I figured out I can increase memory usage for particular program (for example, beauti) through cmd with command: java -Xms600m -Xmx1200m -Djava.library.path=.\lib -cp .\lib\beast.jar beast.app.beauti.BeautiLauncher. I hope this will help other begginers, struggling with java-googleing :)

For Remco: This helps a little, but stil takes awfully long to open file, I still can not access Messages and it freezes from time to time. Then I tried to open the same file, and also files twice as large, with BEAST 2.4.8 - no problem at all. If this is of any help.

Greetings,

Špela

 

Dne sreda, 30. maj 2018 20.05.48 UTC+2 je oseba Špela Borko napisala:

[Remco Bouckaert]

Hi Špela,

Thanks for the update — for v2.5.0 the memory setttings are indeed ignored (I created an issue #784 for that bug).

You can start without using the launcher like so

java -Xms600m -Xmx1200m -Djava.library.path=.\lib -cp .\lib\beast.jar beast.app.beauti.Beauti

but if you have packages installed, then you also should be able to load them using

java -Dbeast.load.jars=true -Xms600m -Xmx1200m -Djava.library.path=.\lib -cp .\lib\beast.jar beast.app.beauti.Beauti

provided you use Java 8 (this does not work with Java 9 or 10).

Cheers,

Remco