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VariantFiltration bug in 3.7? ' input string: "7.902" '

mmats010mmats010 Riverside CAMember
edited May 2017 in Ask the GATK team

Hello,
While trying to filter a file in version 3.7, I got a strange error:

INFO 19:05:58,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO 19:05:58,582 ProgressMeter - | processed | time | per 1M | | total | remaining 
INFO 19:05:58,582 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime 
##### ERROR --
##### ERROR stack trace 
java.lang.NumberFormatException: For input string: "7.902"
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: "7.902"
##### ERROR ------------------------------------------------------------------------------------------

After reverting to version 3.6, the tool ran as expected. I haven't seen any useful posts relating GATK with this error message, so I thought I'd post it here.

Source code:

java -Xmx20g -jar $GATK -T VariantFiltration -R $REF \
-o cross20_flitered_rawE.vcf \
-V allCross20_unflitered_update2_pacBio.vcf \
--filterExpression "FS > 60" \
--filterName "High FischerStrand" \
--filterExpression "SOR > 3" \
--filterName "High StrandOddsRatio" \
--filterExpression "MQ < 40" \
--filterName "Low RMS Mapping Quality" \
--filterExpression "MQRankSum < -12.5" \
--filterName "Low MQRankSum" \
--filterExpression "ReadPosRankSum < -8" \
--filterName "Variant read position bias" \
--filterExpression "QUAL > 30.0 && QUAL < 80.0 " \
--filterName "LowQual" \
--filterExpression "QD < 2" \
--filterName "LowQD"

-Mike

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