Hi there !
I'm having the following error message (see below) when using VariantFiltration (GATK version 3.7.0).
I have used this same code before without having any trouble.
Any help welcome ! I'm stuck. I attach the VCF file I'm trying to annotate as the error seems to be in there...
Cheers,
Adrien
command
java -Xms4G -Xmx4G -jar /gs7k1/home/arieux/Softwares/GATK/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R /gs7k1/home/arieux/Data/Xcc/ref/306/ref_306.fasta \
--variant test.vcf \
-o test.annotated.vcf \
--filterExpression "RA>0.1" --filterName "Heteroplastic" \
--filterExpression "prof<15" --filterName "Low_depth" \
--filterExpression "QUAL <= 0 || MQ <= 1" --filterName "Bad_mapping"
error message
INFO 12:43:00,472 HelpFormatter - -----------------------------------------------------------------------------------
INFO 12:43:00,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 12:43:00,476 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 12:43:00,476 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 12:43:00,477 HelpFormatter - [Thu Jun 08 12:43:00 CEST 2017] Executing on Linux 2.6.32-504.16.2.el6.x86_64 amd64
INFO 12:43:00,477 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13
INFO 12:43:00,483 HelpFormatter - Program Args: -T VariantFiltration -R /gs7k1/home/arieux/Data/Xcc/ref/306/ref_306.fasta --variant 160930_SNK268_B_L008_JBO-8b.vcf -o 160930_SNK268_B_L008_JBO-8b.annotated.vcf --filterExpression RA>0.1 --filterName Heteroplastic --filterExpression prof<15 --filterName Low_depth --filterExpression QUAL <= 0 || MQ <= 1 --filterName Bad_mapping
INFO 12:43:00,490 HelpFormatter - Executing as arieux@cc2-bigmem2 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13.
INFO 12:43:00,491 HelpFormatter - Date/Time: 2017/06/08 12:43:00
INFO 12:43:00,494 HelpFormatter - -----------------------------------------------------------------------------------
INFO 12:43:00,494 HelpFormatter - -----------------------------------------------------------------------------------
INFO 12:43:00,527 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:43:00,644 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
WARN 12:43:00,705 RMDTrackBuilder - Index file /work/arieux/X.citrii.Fasteris2016/test_herbarium/data_merged/new_pipeline/test_problem_python/160930_SNK268_B_L008_JBO-8b.vcf.idx is out of date (index older than input file), deleting and updating the index file
INFO 12:43:00,912 RMDTrackBuilder - Writing Tribble index to disk for file /work/arieux/X.citrii.Fasteris2016/test_herbarium/data_merged/new_pipeline/test_problem_python/160930_SNK268_B_L008_JBO-8b.vcf.idx
INFO 12:43:01,070 GenomeAnalysisEngine - Preparing for traversal
INFO 12:43:01,071 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:43:01,072 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:43:01,072 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:43:01,073 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
ERROR --
ERROR stack trace
java.lang.NumberFormatException: For input string: "44.00"
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.lessThanOrEqual(JexlArithmetic.java:807)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:956)
at org.apache.commons.jexl2.parser.ASTLENode.jjtAccept(ASTLENode.java:18)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:1283)
at org.apache.commons.jexl2.parser.ASTOrNode.jjtAccept(ASTOrNode.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)