Entering edit mode
3.0 years ago
wangh920
▴
10
Anyone would like to help me why this happen when I am running Beagle for imputation. Thanks a lot.
[san331@gra812 BEAGLE-Genetic-Diversity]$ java -jar beagle.17Apr21.dc6.jar gt=Genetic.format.change.vcf.gz out=out.gt
beagle.17Apr21.dc6.jar (version 5.2)
Copyright (C) 2014-2021 Brian L. Browning
Enter "java -jar beagle.17Apr21.dc6.jar" to list command line argument
Start time: 01:59 PM EDT on 19 Apr 2021
Command line: java -Xmx29694m -jar beagle.17Apr21.dc6.jar
gt=Genetic.format.change.vcf.gz
out=out.gt
No genetic map is specified: using 1 cM = 1 Mb
Reference samples: 0
Study samples: 252
Window 1 [chr1.1:294553-40290430]
Reference markers: 411
Study markers: 411
Burnin iteration 1: 4 seconds
Burnin iteration 2: 1 second
Burnin iteration 3: 1 second
Phasing iteration 1: 1 second
Phasing iteration 2: 1 second
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Window 2 [chr1.1:38225303-77746101]
Reference markers: 273
Study markers: 273
Burnin iteration 1: 1 second
Burnin iteration 2: 1 second
Burnin iteration 3: 0 seconds
Phasing iteration 1: 0 seconds
Phasing iteration 2: 0 seconds
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Window 3 [chr1.1:75668792-82444440]
Reference markers: 25
Study markers: 25
Burnin iteration 1: 0 seconds
Burnin iteration 2: 0 seconds
Burnin iteration 3: 0 seconds
Phasing iteration 1: 0 seconds
Phasing iteration 2: 0 seconds
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Window 4 [chr1.2:395660-40019714]
Reference markers: 340
Study markers: 340
Burnin iteration 1: 2 seconds
Burnin iteration 2: 1 second
Burnin iteration 3: 1 second
Phasing iteration 1: 0 seconds
Phasing iteration 2: 0 seconds
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Window 5 [chr1.2:37824204-78270518]
Reference markers: 271
Study markers: 271
Burnin iteration 1: 1 second
Burnin iteration 2: 0 seconds
Burnin iteration 3: 0 seconds
Phasing iteration 1: 0 seconds
Phasing iteration 2: 0 seconds
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Window 6 [chr1.2:75742265-86507080]
Reference markers: 61
Study markers: 61
Burnin iteration 1: 0 seconds
Burnin iteration 2: 0 seconds
Burnin iteration 3: 0 seconds
Phasing iteration 1: 0 seconds
Phasing iteration 2: 0 seconds
Phasing iteration 3: 0 seconds
Phasing iteration 4: 0 seconds
Phasing iteration 5: 0 seconds
Phasing iteration 6: 0 seconds
Phasing iteration 7: 0 seconds
Phasing iteration 8: 0 seconds
Phasing iteration 9: 0 seconds
Phasing iteration 10: 0 seconds
Phasing iteration 11: 0 seconds
Phasing iteration 12: 0 seconds
Exception in thread "main" java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: invalid array
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:593)
at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:735)
at java.util.stream.Nodes.collect(Nodes.java:328)
at java.util.stream.ReferencePipeline.evaluateToNode(ReferencePipeline.java:109)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:541)
at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
at java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:505)
at phase.Stage2Haps.stage2Haps(Stage2Haps.java:141)
at phase.PhaseLS.runStage2(PhaseLS.java:269)
at main.Main.phaseStage2Variants(Main.java:209)
at main.Main.phaseTarg(Main.java:182)
at main.Main.phaseAndImpute(Main.java:171)
at main.Main.main(Main.java:126)
Caused by: java.lang.IllegalArgumentException: invalid array
at vcf.LowMafRefGTRec.throwArrayError(LowMafRefGTRec.java:149)
at vcf.LowMafRefGTRec.checkIndicesAndReturnMajorAllele(LowMafRefGTRec.java:143)
at vcf.LowMafRefDiallelicGTRec.<init>(LowMafRefDiallelicGTRec.java:129)
at vcf.RefGTRec.hapCodedInstance(RefGTRec.java:113)
at phase.Stage2Haps.recs(Stage2Haps.java:167)
at phase.Stage2Haps.lambda$stage2Haps$1(Stage2Haps.java:140)
at java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:269)
at java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:250)
at java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
at java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2183)
at java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2149)
at java.util.stream.AbstractTask.compute(AbstractTask.java:327)
at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
