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java.lang.NumberFormatException when trying to perform VariantFiltration

I'm trying to get a set of robust variants to use to recalibrate quality scores. I called variants using gatk4, and then tried to perform VariantFiltration:

gatk-4.0.5.1/gatk VariantFiltration -R data/genome.fasta -V variants/6753_12-15-2015_first_pass_filtered.vcf -filter 'QD > 2 && FS > 60 && SOR < 3 && MQ > 40 && MQRankSum > -3 && ReadPosRankSum > -4' -output variants/6753_12-15-2015_second_pass_filtered.vcf -filter-name "default"

However, it complains with a java.lang.NumberFormatException:

Using GATK jar gatk-4.0.5.1/gatk-package-4.0.5.1-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 -jar gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar VariantFiltration -R data/genome.fasta -V variants/6753_12-15-2015_first_pass_filtered.vcf -filter QD > 2 && FS > 60 && SOR < 3 && MQ > 40 && MQRankSum > -3 && ReadPosRankSum > -4 -output variants/6753_12-15-2015_second_pass_filtered.vcf -filter-name default
15:42:33.964 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:gatk-4.0.5.1/gatk-package-4.0.5.1-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
15:42:34.114 INFO VariantFiltration - ------------------------------------------------------------
15:42:34.115 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.0.5.1
15:42:34.115 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
15:42:34.115 INFO VariantFiltration - Executing as [email protected] on Mac OS X v10.13.5 x86_64
15:42:34.116 INFO VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_91-b14
15:42:34.116 INFO VariantFiltration - Start Date/Time: June 15, 2018 3:42:33 PM PDT
15:42:34.116 INFO VariantFiltration - ------------------------------------------------------------
15:42:34.116 INFO VariantFiltration - ------------------------------------------------------------
15:42:34.117 INFO VariantFiltration - HTSJDK Version: 2.15.1
15:42:34.118 INFO VariantFiltration - Picard Version: 2.18.2
15:42:34.118 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:42:34.118 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:42:34.118 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:42:34.118 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:42:34.118 INFO VariantFiltration - Deflater: IntelDeflater
15:42:34.119 INFO VariantFiltration - Inflater: IntelInflater
15:42:34.119 INFO VariantFiltration - GCS max retries/reopens: 20
15:42:34.119 INFO VariantFiltration - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
15:42:34.119 INFO VariantFiltration - Initializing engine
15:42:34.634 INFO FeatureManager - Using codec VCFCodec to read file file:///Users/sherlock/dev/Bhatt_lab/crassphage/variants/6753_12-15-2015_first_pass_filtered.vcf
15:42:34.663 INFO VariantFiltration - Done initializing engine
15:42:34.750 INFO ProgressMeter - Starting traversal
15:42:34.750 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:42:34.781 INFO VariantFiltration - Shutting down engine
[June 15, 2018 3:42:34 PM PDT] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=342884352
java.lang.NumberFormatException: For input string: "26.67"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.parseLong(Long.java:631)
at org.apache.commons.jexl2.JexlArithmetic.toLong(JexlArithmetic.java:906)
at org.apache.commons.jexl2.JexlArithmetic.compare(JexlArithmetic.java:718)
at org.apache.commons.jexl2.JexlArithmetic.greaterThan(JexlArithmetic.java:790)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:796)
at org.apache.commons.jexl2.parser.ASTGTNode.jjtAccept(ASTGTNode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:449)
at org.apache.commons.jexl2.parser.ASTAndNode.jjtAccept(ASTAndNode.java:18)
at org.apache.commons.jexl2.Interpreter.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:186)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:95)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:338)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:380)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:339)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.apply(VariantFiltration.java:299)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:109)
at java.util.stream.ForEachOps$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:107)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:994)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
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)

I don't really know how to fix it. ValidateVariants gives no errors, and I am able to perform variant selection, e.g.:

gatk-4.0.5.1/gatk SelectVariants -R data/genome.fasta -V variants/6753_12-15-2015_first_pass_raw.vcf -select 'vc.getGenotype("6753_12-15-2015").getAD().1/vc.getGenotype("6753_12-15-2015").getDP() > 0.9 ' -output variants/6753_12-15-2015_first_pass_filtered.vcf

with no problems. Insights would be gratefully appreciated.
Thanks!
Gavin

Issue · Github
by Sheila

Issue Number
4921
State
closed
Last Updated
Assignee
Array
Closed By
chandrans

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