$java -jar $gatk -T VariantFiltration -R /storage/sandesh/TargetSpot/genome/Corca1_AssemblyScaffolds.fa -o snpsDP10.vcf --variant snps.vcf --genotypeFilterExpression "DP < 9" --genotypeFilterName "DP"
INFO 09:54:10,717 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:54:10,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 09:54:10,720 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 09:54:10,721 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 09:54:10,721 HelpFormatter - [Wed Aug 03 09:54:10 EDT 2016] Executing on Linux 3.13.0-88-generic amd64
INFO 09:54:10,722 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13 JdkDeflater
INFO 09:54:10,728 HelpFormatter - Program Args: -T VariantFiltration -R /storage/sandesh/TargetSpot/genome/Corca1_AssemblyScaffolds.fa -o snpsDP10.vcf --variant snps.vcf --genotypeFilterExpression DP < 9 --genotypeFilterName DP
INFO 09:54:10,732 HelpFormatter - Executing as sshrest1@PlantDestroyer on Linux 3.13.0-88-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13.
INFO 09:54:10,733 HelpFormatter - Date/Time: 2016/08/03 09:54:10
INFO 09:54:10,733 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:54:10,733 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:54:10,752 GenomeAnalysisEngine - Strictness is SILENT
INFO 09:54:10,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 09:54:11,179 GenomeAnalysisEngine - Preparing for traversal
INFO 09:54:11,183 GenomeAnalysisEngine - Done preparing for traversal
INFO 09:54:11,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 09:54:11,185 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 09:54:11,186 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
ERROR --
ERROR stack trace
java.lang.IllegalArgumentException: Invalid JEXL expression detected for DP with message no message
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:136)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:93)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:22)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:323)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:433)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:349)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.map(VariantFiltration.java:97)
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:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:255)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:157)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)