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Variant Filter error

nansnans Member
edited March 2017 in Ask the GATK team

Hello, I am running the Variant Filter command as follows

java -Xmx40g -jar GenomeAnalysisTK.jar -T VariantFiltration \
-R g1k.fasta \
-V merged_samples_recalSNPs.vcf \
-G_filter "GQ < 30.0 || DP < 10" \
-G_filterName ‘LowQ’ \
-o merged_samples_fil_SNPs.vcf

But I end up with an error

INFO 11:06:38,367 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 11:06:38,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 11:06:38,371 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 11:06:38,371 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 11:06:38,371 HelpFormatter - [Tue Mar 21 11:06:38 GMT 2017] Executing on Linux 2.6.32-642.11.1.el6.Bull.106.x86_64 amd64
INFO 11:06:38,371 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 JdkDeflater
INFO 11:06:38,377 HelpFormatter - Program Args: -T VariantFiltration -R g1k.fasta -V merged_samples_recalSNPs.vcf -G_filter GQ < 30.0 || DP < 10 -G_filterName LowQ -o merged_samples_fil_SNPs.vcf
INFO 11:06:38,382 HelpFormatter - Executing as [email protected] on Linux 2.6.32-642.11.1.el6.Bull.106.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 11:06:38,382 HelpFormatter - Date/Time: 2017/03/21 11:06:38
INFO 11:06:38,383 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 11:06:38,383 HelpFormatter - -------------------------------------------------------------------------------------------
INFO 11:06:38,408 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:06:38,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:06:38,838 GenomeAnalysisEngine - Preparing for traversal
INFO 11:06:38,844 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:06:38,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:06:38,846 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:06:38,846 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:07:08,849 ProgressMeter - 1:15710411 5800.0 30.0 s 86.2 m 0.5% 98.7 m 98.2 m
INFO 11:07:38,851 ProgressMeter - 1:38003363 13223.0 60.0 s 75.6 m 1.2% 81.6 m 80.6 m
INFO 11:08:08,852 ProgressMeter - 1:90048248 20498.0 90.0 s 73.2 m 2.9% 51.7 m 50.2 m
INFO 11:08:38,853 ProgressMeter - 1:152277528 27336.0 120.0 s 73.2 m 4.9% 40.7 m 38.7 m
INFO 11:09:08,854 ProgressMeter - 1:180000516 35049.0 2.5 m 71.3 m 5.8% 43.1 m 40.6 m
INFO 11:09:38,855 ProgressMeter - 1:227174408 42212.0 3.0 m 71.1 m 7.3% 41.0 m 38.0 m
INFO 11:10:08,856 ProgressMeter - 2:27423962 49345.0 3.5 m 70.9 m 8.9% 39.2 m 35.7 m
INFO 11:10:38,857 ProgressMeter - 2:86000012 56719.0 4.0 m 70.5 m 10.8% 37.0 m 33.0 m
INFO 11:11:08,858 ProgressMeter - 2:145146416 64007.0 4.5 m 70.3 m 12.7% 35.4 m 30.9 m
INFO 11:11:38,859 ProgressMeter - 2:203682178 71256.0 5.0 m 70.2 m 14.6% 34.2 m 29.2 m
INFO 11:12:08,860 ProgressMeter - 2:242062334 78475.0 5.5 m 70.1 m 15.8% 34.7 m 29.2 m
INFO 11:12:38,865 ProgressMeter - 3:48461313 85680.0 6.0 m 70.0 m 17.4% 34.4 m 28.4 m
INFO 11:13:08,866 ProgressMeter - 3:119013714 93117.0 6.5 m 69.8 m 19.7% 33.0 m 26.5 m
INFO 11:13:38,867 ProgressMeter - 3:183774762 100207.0 7.0 m 69.9 m 21.8% 32.1 m 25.1 m
INFO 11:14:08,868 ProgressMeter - 4:15003513 107660.0 7.5 m 69.7 m 22.7% 33.0 m 25.5 m
INFO 11:14:38,873 ProgressMeter - 4:104000917 114823.0 8.0 m 69.7 m 25.6% 31.2 m 23.2 m

ERROR --
ERROR stack trace

java.lang.IllegalArgumentException: Invalid JEXL expression detected for LowQ 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)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
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://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Invalid JEXL expression detected for LowQ with message no message
ERROR ------------------------------------------------------------------------------------------

Any suggestions to get this working ?

Many thanks

Answers

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