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A problem met when running Mutect2 4.0.9.0

14:44:03.509 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 14.865818774000001
14:44:03.509 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 3144.705825942
14:44:03.509 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1498.35 sec
14:44:03.511 INFO Mutect2 - Shutting down engine
[March 4, 2019 2:44:03 PM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 276.83 minutes.
Runtime.totalMemory()=4570218496
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$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
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.GermlineProbabilityCalculator.getGermlineAltAlleleFrequencies(GermlineProbabilityCalculator.java:49)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.getPopulationAFAnnotation(GermlineProbabilityCalculator.java:27)
at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:151)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:217)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:215)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:291)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
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)
Using GATK jar /hwfssz1/ST_PRECISION/PMO/F16ZQSB1SY2968/3.scripts/5.WESpipeline/software/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx8g -XX:ParallelGCThreads=1 -Dsamjdk.compression_level=5 -XX:-UseGCOverheadLimit -Djava.io.tmpdir=tmp_dir -jar /mydir/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar Mutect2 -R /mydir/database/reference/grch37.fa -I /mydir/Tumor.bqsr.bam -tumor Tumor -I /mydir/Normal.bqsr.bam -normal Normal --germline-resource /mydir/GATK_bundle/gnomAD/exomes/gnomad.exomes.r2.0.2.sites.vcf.gz -L /mydir/allchr.intervals -O /mydir/mutect2.vcf.gz

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