Help fix error message in beagle 4

kikikiki UIUCMember

Hi, I am trying to impute missing SNPs using beagle4. However, I am getting the error message, Could you help please?

No genetic map is specified: using 1 cM = 1 Mb Exception in thread "main" java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 5:35101444 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:422) 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.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at vcf.VcfIt.fillEmissionBuffer(VcfIt.java:307) at vcf.VcfIt.next(VcfIt.java:363) at vcf.VcfIt.next(VcfIt.java:52) at vcf.IntervalVcfIt.readFirstRecord(IntervalVcfIt.java:99) at vcf.IntervalVcfIt.(IntervalVcfIt.java:59) at main.Main.nonRefData(Main.java:261) at main.Main.main(Main.java:111) Caused by: java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 5:35101444 at vcf.BasicMarker.checkAlleles(BasicMarker.java:130) at vcf.BasicMarker.extractAlleles(BasicMarker.java:312) at vcf.BasicMarker.(BasicMarker.java:249) at vcf.VcfRecGTParser.(VcfRecGTParser.java:70) at vcf.BitSetGT.(BitSetGT.java:74) at vcf.VcfIt.lambda$static$6(VcfIt.java:90) at vcf.VcfIt.lambda$new$7(VcfIt.java:192) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747) at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721) at java.util.stream.AbstractTask.compute(AbstractTask.java:316) at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731) at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289) at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056) at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692) at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

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