Error when Phasing with Beagle 5.2

Error when Phasing with Beagle 5.2


I’m having trouble phasing a multi-sample (9-samples) vcf file produced by gatk HaplotypeCaller with Beagle 5.2. I do not have a genetic map or reference panel. I am working with a very heterozygous group of organisms (sea urchins). When I run beagle with the following command,

java -Xmx100g -jar beagle_5.2.jar gt=filtered_calls.vcf.gz out=phased impute=false

I get this error:

    Window 470 [NW_022145483.1:11416-24979]
    Reference markers:                  630
    Study     markers:                  630
    Burnin  iteration 1:           0 seconds
    Exception in thread "main" java.lang.IllegalArgumentException: 0
            at main.RunStats.printEstimatedNe(
            at main.Main.phaseStage1Variants(
            at main.Main.phaseTarg(
            at main.Main.phaseAndImpute(
            at main.Main.main(

Beagle usually runs fine for about 15 min and outputs 1.4G of phased genotypes, then crashes. I’m not sure what this error code means. I have been playing around with memory usage and window size (anywhere between 5 and 40). Neither has seemed to help. When I change the window size, it crashes while processing different scaffolds. I’m fairly sure that there isn’t a problem with my input vcf file as other programs have run successfully using it as input.

Are there other programs that will phase without a genetic map and reference panel? Should I split my vcf files into separate files for each chromosome before phasing with Beagle? I have access to HPC so memory should not be an issue.







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