ERROR MESSAGE: For input string: "0.000" - Variantfiltration - GATK 3.7-0

mveyssieremveyssiere EvryMember
edited January 2017 in Ask the GATK team

Hi,
I encountered an issue with the current version of GATK. I received the following error message :
ERROR MESSAGE: For input string: "0.000",
when I ran this command :
'java -Xmx2g -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg19.fa -o annotQ.vcf -V chr1.vcf -filter "DP < 12" --filterName "DPFilter" -filter "MQ < 30" --filterName "MQFilter" -filter "QD < 2" --filterName "QDFilter" -filter "FS > 25" --filterName "FSFilter" -filter "DP < 12" --filterName "DPgenotype".

This "0.000" value is an FS value and when I removed all the lines containing it, I encountered the same error for an other value.

It has to be noticed that I do not have this error with a previous version of GATK (3.4-46) in the same environment and with exactly the same command.

Is there something I should have changed in my command when I moved to the current version of GATK ?
Here is the trace :

ERROR --
ERROR stack trace

java.lang.NumberFormatException: For input string: "0.000"
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.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:178)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:94)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:341)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:483)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.buildVCfilters(VariantFiltration.java:474)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:379)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:318)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:99)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: For input string: "0.000"
ERROR ------------------------------------------------------------------------------------------

Thanks for your help

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