gVCF文件转换成VCF格式时,已经在后台运行了很久了,突然程序关闭了,报错信息显示:

16:11:06.922 INFO  GenotypeGVCFs - Shutting down engine

[2023年12月4日 下午04时11分06秒] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 2,326.36 minutes.

Runtime.totalMemory()=19664470016

java.lang.IllegalStateException: No likelihood sum exceeded zero -- method was called for variant data with no variant information.

        at org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils.calculateMostLikelyAlleles(AlleleSubsettingUtils.java:31>

        at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:137)

        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.calculateGenotypes(GenotypeGVCFsEngine.java:244)

        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:152)

        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:135)

        at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:283)

        at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:135)

        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)

        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)

        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)

        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)

        at java.util.Iterator.forEachRemaining(Iterator.java:116)

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

这个需要检查数据是否有问题呢,

如果没问题,重新运行

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  • shidandan 提出于 2023-12-05 09:24

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