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Why is gatk4 GetPileupSummaries always failed ?

Binfls6321DTUBinfls6321DTU Member
edited October 2017 in Ask the GATK team

I used the following command

/home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-launch --javaOptions "-Xmx20g" GetPileupSummaries \
-R /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta \
-I tumor.bam \
-V /home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz \
-O /home/projects/cu_10098/data/ennbin/project/hg37_testWithNewgnomAD/filtration_test/GetPileupSummaries.table

and it always fails, and I cant find where the error is.......
the error message is shown below:

Using GATK jar /home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-package-4.beta.5-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=1 -Dsnappy.disable=true -Xmx20g -jar /home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-package-4.beta.5-local.jar GetPileupSummaries -R /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta -I tumor.bam -V /home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz -O /home/projects/cu_10098/data/ennbin/project/hg37_testWithNewgnomAD/filtration_test/GetPileupSummaries.table
19:19:21.288 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/projects/cu_10098/apps/src/gatk-4.beta.5/gatk-package-4.beta.5-local.jar!/com/intel/gkl/native/libgkl_compression.so
[October 9, 2017 7:19:21 PM CEST] GetPileupSummaries --output /home/projects/cu_10098/data/ennbin/project/hg37_testWithNewgnomAD/filtration_test/GetPileupSummaries.table --variant /home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz --input tumor.bam --reference /home/databases/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta --minimumPopulationAlleleFrequency 0.01 --maximumPopulationAlleleFrequency 0.2 --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --interval_merging_rule ALL --readValidationStringency SILENT --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --createOutputBamMD5 false --createOutputVariantIndex true --createOutputVariantMD5 false --lenient false --addOutputSAMProgramRecord true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disableBamIndexCaching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --gcs_max_retries 20 --disableToolDefaultReadFilters false
[October 9, 2017 7:19:21 PM CEST] Executing as ennbin@computerome01 on Linux 3.10.0-514.10.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_144-b01; Version: 4.beta.5
19:19:21.429 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 1
19:19:21.429 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:19:21.429 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:19:21.429 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:19:21.429 INFO GetPileupSummaries - Deflater: IntelDeflater
19:19:21.429 INFO GetPileupSummaries - Inflater: IntelInflater
19:19:21.429 INFO GetPileupSummaries - GCS max retries/reopens: 20
19:19:21.429 INFO GetPileupSummaries - Using google-cloud-java patch c035098b5e62cb4fe9155eff07ce88449a361f5d from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
19:19:21.429 INFO GetPileupSummaries - Initializing engine
19:19:22.766 INFO FeatureManager - Using codec VCFCodec to read file file:///home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz
19:19:23.569 INFO FeatureManager - Using codec VCFCodec to read file file:///home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz
19:19:25.109 WARN IndexUtils - Feature file "/home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:19:25.184 WARN IndexUtils - Feature file "/home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:19:25.219 WARN IndexUtils - Feature file "/home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:19:25.254 WARN IndexUtils - Feature file "/home/projects/cu_10098/data/public_data/gnomad.exomes.r2.0.2.sites.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
19:19:25.292 INFO GetPileupSummaries - Done initializing engine
19:19:25.292 INFO ProgressMeter - Starting traversal
19:19:25.293 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:19:25.310 INFO GetPileupSummaries - Shutting down engine
[October 9, 2017 7:19:25 PM CEST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=1781006336
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.getAttributeAsDouble(CommonInfo.java:323)
at htsjdk.variant.variantcontext.VariantContext.getAttributeAsDouble(VariantContext.java:732)
at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.alleleFrequencyInRange(GetPileupSummaries.java:111)
at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.apply(GetPileupSummaries.java:94)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:838)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.j>ava:176)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:195)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)
at org.broadinstitute.hellbender.Main.main(Main.java:233)

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