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Bug when filtering INDELs?

Hi guys
I am using GAT3.7, I subsetted my SNPs and Indels, filtered the SNPs and then wanted to run my filters on the Indels but get an error that looks like a bug, here the log file

INFO 09:54:57,570 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:54:57,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 09:54:57,573 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 09:54:57,573 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 09:54:57,574 HelpFormatter - [Wed Feb 01 09:54:57 CET 2017] Executing on Linux 2.6.32-642.6.2.el6.x86_64 amd64
INFO 09:54:57,575 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14
INFO 09:54:57,577 HelpFormatter - Program Args: -T VariantFiltration -R /scicore/home/salzburg/boehne/Reference_Oniloticus_Micha/reference/GCF_001858045.1_ASM185804v2_genomic_edit.fna
-V /scicore/home/salzburg/boehne/Ambizione/Aburtoni_pops_genomes/GATK3.7_OrenilV2/CatVariantsFinal/AllChrs_GATK3.7_40alleles_addAnnot_INDELs2.vcf --filterName QualityByDepth --filterExp
ression QD < 2.0 --filterName StrandBias --filterExpression FS > 200.0 --filterName ReadPosRankSum --filterExpression ReadPosRankSum < -20.0 --filterName StrandOddsRatio --filterExpress
ion SOR > 10 --filterName LowDepth --filterExpression DP < 1500 --filterName HighDepth --filterExpression DP > 12813 -o /scicore/home/salzburg/boehne/Ambizione/Aburtoni_pops_genomes/GAT
K3.7_OrenilV2/FilterSNPandIndel/AllChrs_GATK3.7_40alleles_INDELs_filtered.vcf
INFO 09:54:57,586 HelpFormatter - Executing as [email protected] on Linux 2.6.32-642.6.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14.
INFO 09:54:57,586 HelpFormatter - Date/Time: 2017/02/01 09:54:57
INFO 09:54:57,586 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:54:57,587 HelpFormatter - ---------------------------------------------------------------------------------
INFO 09:54:57,615 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:54:57,707 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:54:58,009 GenomeAnalysisEngine - Preparing for traversal
INFO 09:54:58,019 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:54:58,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:54:58,020 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:54:58,020 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

ERROR --
ERROR stack trace

java.lang.NumberFormatException: For input string: "2.303"
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: "2.303"
ERROR ------------------------------------------------------------------------------------------

Thanks for help
Astrid

Answers

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