limitations to the number of individuals for microsatellite analyses

[RH]

Dear all,

I am trying, quite unsuccessfully, to run BEAST on a dataset with 908 individuals and 9 microsatellite loci. When I use the complete dataset it gives me several errors, saying it can't parse the values. However, if I trim my dataset to 240 individuals it runs without a glitch

Has anyone experienced the same? And do you know if there is a way to circumvent this problem? I think BSP and tmrca estimates will be better if I use my complete dataset...

thank you.

cheers,

Romina 

[Heather Baldwin]

Hi Romina,

Have you checked and double-checked the data file for errors? It sounds to me like there is probably a minor error in the larger data file that doesn't occur in the subset file, like a missing value or incorrect syntax somewhere. 

Good luck with it,

Heather

[RH]

Hi Heather,

Thank you for your advice. But I don't think there is an error in the file. I have tried to remove loci (the ones indicated as problematic) and re-run, and still nothing happens. It only runs when I randomly decrease the number of individuals. This is the error I am getting:

Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser

line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser

Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

Parsing XML file: capensisBEAST1.xml

  File encoding: Cp1252

Looking for plugins in C:\Users\rhenriques\Desktop\plugins

Fatal exception: 88

can not be converted. State needs to be an integer or unknown (?).

java.lang.NumberFormatException: 88

can not be converted. State needs to be an integer or unknown (?).

at dr.evolution.datatype.Microsatellite.getState(Unknown Source)

at dr.evoxml.MicrosatellitePatternParser.parseXMLObject(Unknown Source)

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)

java.lang.RuntimeException: Terminate

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

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

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

The 88 the system is referring to is the repetition unit number of locus 3, which runs perfectly when I have a smaller number of individuals.

Any help with this would be much appreciated!

cheers,

Romina

[Heather]

Hi Romina,

then I have no idea what the problem could be, sorry. Good luck with it!

[RH]

Thanks Heather! 

I just emailed one of the authors, hopefully he will be able to help me (or tell me I'm being an idiot...).

cheers,

Romina

[Cilia Antoniou]

Hi Romina,

did you get an answer?
I seem to have the same problem as you did.
Please advise
Cheers,
Cilia

[Romina Henriques]

Hi Cilia,

No, he answered the first email, but never got back to me with a solution. I ended up not using BEAST in the end.

Please, let me know if you have better luck.

cheers,

Romina

--
You received this message because you are subscribed to a topic in the Google Groups "beast-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/beast-users/aV_Bngdbv2s/unsubscribe.
To unsubscribe from this group and all its topics, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.

Visit this group at https://groups.google.com/group/beast-users.

For more options, visit https://groups.google.com/d/optout.