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Run Mutect2 in gatk-4.0.4.0 with an error `java.lang.NumberFormatException: For input string: "."`

Hi there~

When I ran mutect2 in gatk-4.0.4.0,I got something wrong with it.

gatk --java-options "-Xmx7g -XX:+UseParallelGC -XX:ParallelGCThreads=8" Mutect2 \
--dont-use-soft-clipped-bases true --max-reads-per-alignment-start 3000 --min-base-quality-score 20 \
-R hg19.fasta \
--germline-resource \gnomad.exomes.r2.0.2.sites.vcf.gz \
-I test-1.final.bam  -tumor test-1 \
-O test-1.raw.vcf \
-L agilent.gatk.intervals

It goes error with :

[August 8, 2018 10:27:44 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.34 minutes.

Runtime.totalMemory()=3729260544
java.lang.NumberFormatException: For input string: "."
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at htsjdk.variant.variantcontext.CommonInfo.lambda$getAttributeAsDoubleList$2(CommonInfo.java:299)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Collections$2.tryAdvance(Collections.java:4717)
at java.util.Collections$2.forEachRemaining(Collections.java:4725)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsList(CommonInfo.java:273)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsDoubleList(CommonInfo.java:293)
at htsjdk.variant.variantcontext.VariantContext.getAttributeAsDoubleList(VariantContext.java:740)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.isActive(Mutect2Engine.java:253)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.loadNextAssemblyRegion(AssemblyRegionIterator.java:159)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:135)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.next(AssemblyRegionIterator.java:34)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:290)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:892)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

How can i fix it?

Answers

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