Question: Arrayindex Exception When Running Beagle
gravatar for Tim
6.1 years ago by
Tim0 wrote:


I am using the phasing pipeline provided with the germline and beagle, which converts plink into beagle and then germline files. However, I do get an error message win the BEAGLE software which is the following

Converting to BEAGLE
81843 SNPs
1050 samples
Beagle version 3.0.4

Command line: java -jar beagle.jar 

number of markers    =   81843
number of haplotypes =    2100 (out_5.pre_phase.bgl)

Phasing: iteration 1

Phasing: iteration 2
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -2
    at phaser.Z.c(Unknown Source)
    at phaser.r.a(Unknown Source)
    at phaser.K.a(Unknown Source)
    at phaser.V.a(Unknown Source)
    at phaser.PhaseMain.<init>(Unknown Source)
    at phaser.PhaseMain.main(Unknown Source)
tail: cannot open `out_5.pre_phase.bgl.phased' for reading: No such file or directory
rm: cannot remove `out_5.pre_phase.bgl.phased': No such file or directory line 79: gawk: command not found
Pedigree:    0
Individuals:    0

could anybody point me into the direction of the problem? I think it is important to note that

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -2

but I am not sure what it indicates

java • 2.4k views
ADD COMMENTlink modified 6.1 years ago by Istvan Albert ♦♦ 80k • written 6.1 years ago by Tim0

It could be that the program got something unexpected. Did you try to run BEAGLE with the test data? If you are able to use the test data without any issues, that would help you isolate your problem (and indicate something may be going on with your data).

ADD REPLYlink written 6.1 years ago by SES8.1k

You question is unclear, so if you would like help in this forum it's important to provide us with as much information as possible and follow guidelines. I have used BEAGLE before in the context of BEAST for phylogenetics, but I don't know what germline is, so perhaps in the future you could provide a link or some other information. What have you tried to solve your problem? There's an "out of bounds exception" at phaser? Looks like you are missing an output or pre-packaged file: 'out_5.pre_phase.bgl.phased'. Did you check to see if all the phaser files are present? Are there any errors in these files? Are you using the recommended version of Java for BEAGLE or germline? Tell us what you did already and help us to hone in on your problem.

ADD REPLYlink written 6.1 years ago by Josh Herr5.6k
gravatar for statGen
6.1 years ago by
statGen0 wrote:

Contact Prof. Brian Browning (

He developed BEAGLE and is very responsive.

ADD COMMENTlink written 6.1 years ago by statGen0
gravatar for Tim
6.1 years ago by
Tim0 wrote:

is there anybody who could help me with the question directly because of firs hand expericne wih BEAGLE or anything else?

ADD COMMENTlink written 6.1 years ago by Tim0

please make sure not to add answers when you don't have one, use the comment field to add comments

ADD REPLYlink written 6.1 years ago by Istvan Albert ♦♦ 80k
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