SNAPP (BFD) Error FATAL exception

[Tiamiyu Bashir]

Hi, 

I setup SNAPP for Bayes Factor Delimitation, I ran the .xml file on the cluster and I got this error.

Loading /public/home/WHC_BBT/final_data_set_SNAPP/runA//step0/likelihood.log, burnin 50%, skipping 0 log lines

|---------|---------|---------|---------|---------|---------|---------|---------|

Calculating statistics

|---------|---------|---------|---------|---------|---------|---------|---------|

Fatal exception: 1

java.lang.ArrayIndexOutOfBoundsException: 1

at beast.util.LogAnalyser.calcStats(Unknown Source)

at beast.util.LogAnalyser.<init>(Unknown Source)

at beast.util.LogAnalyser.<init>(Unknown Source)

at beast.inference.PathSampleAnalyser.estimateMarginalLikelihood(Unknown Source)

at beast.inference.PathSampleAnalyser.estimateMarginalLikelihood(Unknown Source)

at beast.inference.PathSampler.analyse(Unknown Source)

at beast.inference.PathSampler.doRuns(Unknown Source)

at beast.inference.PathSampler.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

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

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

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Fatal exception: 1

java.lang.RuntimeException: An error was encounted. Terminating BEAST

at beast.app.util.ErrorLogHandler.publish(Unknown Source)

at java.util.logging.Logger.log(Logger.java:738)

at java.util.logging.Logger.doLog(Logger.java:765)

at java.util.logging.Logger.log(Logger.java:788)

at java.util.logging.Logger.severe(Logger.java:1464)

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

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

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at beast.app.beastapp.BeastLauncher.run(Unknown Source)

at beast.app.beastapp.BeastLauncher.main(Unknown Source)

Kindly help look into to solving this.

Thanks,

Bashir

[Tiamiyu Bashir]

I was able to resolve this, by checking the "" in my path sampling commands, the signs was not recognized, because I copied directly. So I would suggest that it should be typed or look for any of the shared BFD (SNAPP) .xml files already shared on the google group and compare with yours.

I hope this helps lots of folks.

[Alex Krohn]

Hi Bashir,

Can you explain this further, please? I rad SNAPP, then used path sampling (with 50 steps) to calculate a marginal likelihood. It worked for the first 7 steps, but gave this same error at Step 8. It sounds like you had a quote (") out of place. Where exactly was it out place? 

Also, once you figured out which quote to delete, how could you continue the run to only calculate statistics, rather than re-run the entire SNAPP tree?

Thanks,

Alex

[Tiamiyu Bashir]

Hi Alex,

The setup can be tricky, you can check the highlighted parts. Also, you can check mine, for easy viewing, you can open with Notepad++, and compare with yours keenly.

I hope you'll be able to resolve this.

Cheers,

Bashir

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Tiamiyu B. Bashir

Department of Plant Biology,

Faculty of Life Sciences,

University of Ilorin,

Ilorin.

+2348060847600

+2348077078389

[Alex Krohn]

Hmm. That's odd. Mine does have those quotes in it. I'm not sure why it worked for 7 steps, but failed at step 8.

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[Tiamiyu Bashir]

Hi Alex,

I have edited your .xml file, you can try it out and hope it'll work fine.

Cheers,

Bashir

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