Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

A problem met when running Mutect2 4.0.9.0

jemimalwhjemimalwh ChinaMember

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

Tagged:

Best Answers

Answers

Sign In or Register to comment.