TreeAnnotator: Exception in thread "main" java.lang.NumberFormatException

[Michael]

Hi all,

I am using BEAST package v1.10.1. I ran the same xml file for 5 times and got 5 replicates. The chain length of each MCMC run is 500,000,000. I used LogCombiner to combine these 5 log and tree files. The state of the combined file is 2,250,250,000. (My another question: Why is it not 500,000,000 * 5 = 2,500,000,000?)

Then I used TreeAnnotator for the combined tree files. My commend was as follows: 

treeannotator -heights median -burnin 225025000 combined.trees MCC.trees

However, I got an error in the first step “Reading trees.“ The error message was:

Reading trees (bar assumes 10,000 trees)...

0              25             50             75            100

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

******************************************************************************************************************************************************************************************************************************************************************Exception in thread "main" java.lang.NumberFormatException: For input string: "2147500000"

at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.base/java.lang.Integer.parseInt(Integer.java:652)

at java.base/java.lang.Integer.parseInt(Integer.java:770)

at dr.app.tools.TreeAnnotator.<init>(Unknown Source)

at dr.app.tools.TreeAnnotator.main(Unknown Source)

If I set the burnin to 0, then TreeAnnotator worked well. (So, I do not think it was due to not enough memory.) I also tried to set the burnin to different numbers (50000, 214750000, 250000000), but I got the same error message.

Dose anyone know what the problem is and how I can solve this issue?

Best wishes,

Michael

[Alexei Drummond]

Hey Michael,

(1) You have reached the maximum 32 bit signed integer. Numbers greater than 2,147,483,647 can not be represented by a 32 bit signed integer.

(2) I believe the combined file is 2.25 billion because 10% is removed from each replicate when they are being combined.

(3) I think you can ask LogCombiner to renumber your states so that you don’t have this problem of numerical overflow, but I am not sure about the exact options in BEAST 1.

Cheers
Alexei

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[Michael]

Hi Alexei,

Thanks for your swift reply. However, I have some follow-up questions.

(1) You have reached the maximum 32 bit signed integer. Numbers greater than 2,147,483,647 can not be represented by a 32 bit signed integer. 

This makes sense to me, but why did it work if I set burnin to 0 (i.e., not remove burnin)?

However, according to your second command, I think I do not need to remove burnin again because LogCombiner has already done that.

(2) I believe the combined file is 2.25 billion because 10% is removed from each replicate when they are being combined. 

(3) I think you can ask LogCombiner to renumber your states so that you don’t have this problem of numerical overflow, but I am not sure about the exact options in BEAST 1. 

When I used LogCombiner -renumber flag to combine these 5 log/tree files, I got an error message as follows.

My command: logcombiner -renumber 1.log 2.log 3.log 4.log 5.log combined.log

Creating combined log file: 'combined.log'

Renumbering output.

Combining file: '1.log' without removing burnin

Exception in thread "main" java.lang.ArithmeticException: / by zero

at dr.app.tools.LogCombiner.<init>(Unknown Source)

at dr.app.tools.LogCombiner.main(Unknown Source)

I think the error is because LogCombiner tries to divide a number by zero. I suppose this is a bug?

When I changed the first STATE of the first log/tree files from 0 to 1, then it seemed to work well, and I could get the combined log/tree files.

Best wishes,

Michael

[Nick Fountain-Jones]

Hi all,

I'm having the similar problem - anyone any thoughts?

Best,

Nick Fountain-Jones

[Michael]

Hi Nick,

What's the problem you encountered and are you also using BEAST v1.10.1? I kind of know how to deal with it. For LogCombiner, just change the first state of the first log/tree file to 1, then "renumber" works for me. Once the STATE of the tree file doesn't exceed 2,147,483,647, then TreeAnnotator works fine as well.

Best wishes,

Michael

[Andrew Rambaut]

This bug (not being able to parse state numbers in the trees file if > 2,147,483,647) has been fixed and will be in the next release. If you need to try it out, you can download the GitHub repository and build the executables:

https://github.com/beast-dev/beast-mcmc/

Andrew

[Nick Fountain-Jones]

Thanks Andrew and Michael - worked fine.

Best,

Nick

Numering didn't