Java reports an error when running beagle to fill the vcf file
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Entering edit mode
2.1 years ago
yoser4 ▴ 10

Hello everyone

I am a new user of Java. Today, when I was running beagle to populate the snp vcf file, I encountered a Java error.

My code is:

java -Xmx30688m -jar beagle.22Jul22.46e.jar
  gt=input_snps.vcf.gz
  out=output_beagle
  ne=10000
  nthreads=48

The error is:

Window 4 [chr1:114001825-154002784]
Study     markers:              387,782
java.lang.OutOfMemoryError: Java heap space
        at phase.HmmParamData.<init>(HmmParamData.java:73)
        at phase.PhaseLS.lambda$getParamEst$1(PhaseLS.java:129)
        at phase.PhaseLS$$Lambda$535/0x0000000800164c40.run(Unknown Source)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)
java.lang.OutOfMemoryError: Java heap space
        at phase.HmmParamData.<init>(HmmParamData.java:73)
        at phase.PhaseLS.lambda$getParamEst$1(PhaseLS.java:129)
        at phase.PhaseLS$$Lambda$535/0x0000000800164c40.run(Unknown Source)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)

How to solve this error? Any help will be appreciated

vcf beagle Java • 548 views
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