ava.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50]

[elbakrifz]

I have tried with the following CML : java -Xmx4G -jar /Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836\ 4/GenomeAnalysisTK.jar \ -T VariantFiltration \ -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta \ -V /Users/mac/Desktop/NGS-/59variants.vcf \ -o /Users/mac/Desktop/NGS-/59variants.vcf \ --filterExpression "AB < 0.2 || MQ0 > 50"
I get :
INFO 19:41:16,071 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 19:41:16,071 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 19:41:16,072 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 19:41:16,073 HelpFormatter - [Tue Aug 25 19:41:16 WEST 2020] Executing on Mac OS X 10.15.6 x86_64
INFO 19:41:16,073 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17
INFO 19:41:16,080 HelpFormatter - Program Args: -T GenotypeGVCFs -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta -V /Users/mac/Desktop/NGS-/42variants.g.vcf -o /Users/mac/Desktop/NGS-/42variants.vcf
INFO 19:41:16,243 HelpFormatter - Executing as [email protected] on Mac OS X 10.15.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17.
INFO 19:41:16,244 HelpFormatter - Date/Time: 2020/08/25 19:41:16
INFO 19:41:16,245 HelpFormatter - ----------------------------------------------------------------------------------
INFO 19:41:16,245 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836%204/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 19:41:17,138 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 19:41:17,138 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 19:41:17,139 GenomeAnalysisEngine - Strictness is SILENT
INFO 19:41:17,240 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 19:41:17,417 GenomeAnalysisEngine - Preparing for traversal
INFO 19:41:17,419 GenomeAnalysisEngine - Done preparing for traversal
INFO 19:41:17,419 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 19:41:17,420 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 19:41:17,420 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
WARN 19:41:17,540 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
WARN 19:41:17,540 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 19:41:17,541 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
INFO 19:41:17,542 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
WARN 19:41:17,699 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not GenotypeGVCFs
INFO 19:41:47,428 ProgressMeter - LmjF18_01_20050601_V5.2:104301 7741089.0 30.0 s 3.0 s 23.9% 2.1 m 95.0 s
INFO 19:42:17,437 ProgressMeter - LmjF35_01_20050601_V5.2:415001 2.1195519E7 60.0 s 2.0 s 65.8% 91.0 s 31.0 s
INFO 19:42:40,369 ProgressMeter - done 3.2855403E7 82.0 s 2.0 s 100.0% 82.0 s 0.0 s
INFO 19:42:40,370 ProgressMeter - Total runtime 82.95 secs, 1.38 min, 0.02 hours

Done. There were 4 WARN messages, the first 4 are repeated below.
WARN 19:41:17,540 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
WARN 19:41:17,540 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 19:41:17,541 StrandBiasTest - StrandBiasBySample annotation exists in input VCF header. Attempting to use StrandBiasBySample values to calculate strand bias annotation values. If no sample has the SB genotype annotation, annotation may still fail.
WARN 19:41:17,699 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not GenotypeGVCFs

(base) MacBook-Air-de-mac:~ mac$ java -Xmx4G -jar /Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836\ 4/GenomeAnalysisTK.jar \ -T VariantFiltration \ -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta \ -V /Users/mac/Desktop/NGS-/59variants.vcf \ -o /Users/mac/Desktop/NGS-/59variants.vcf \ --filterExpression "AB < 0.2 || MQ > 50"
INFO 11:26:16,702 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:26:16,710 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 11:26:16,710 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 11:26:16,711 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 11:26:16,711 HelpFormatter - [Wed Aug 26 11:26:16 WEST 2020] Executing on Mac OS X 10.15.6 x86_64
INFO 11:26:16,712 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17
INFO 11:26:16,716 HelpFormatter - Program Args: -T VariantFiltration -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta -V /Users/mac/Desktop/NGS-/59variants.vcf -o /Users/mac/Desktop/NGS-/59variants.vcf --filterExpression AB < 0.2 || MQ > 50
INFO 11:26:16,926 HelpFormatter - Executing as [email protected] on Mac OS X 10.15.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17.
INFO 11:26:16,927 HelpFormatter - Date/Time: 2020/08/26 11:26:16
INFO 11:26:16,927 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:26:16,928 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836%204/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 11:26:19,995 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 11:26:19,996 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 11:26:19,996 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:26:20,255 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:26:20,788 GenomeAnalysisEngine - Preparing for traversal
INFO 11:26:20,789 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:26:20,789 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:26:20,790 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:26:20,790 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

ERROR --

ERROR stack trace

java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ > 50]
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:238)
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.initialize(VariantFiltration.java:251)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
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 3.8-0-ge9d806836):

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: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ > 50]

ERROR ------------------------------------------------------------------------------------------

(base) MacBook-Air-de-mac:~ mac$ java -Xmx4G -jar /Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836\ 4/GenomeAnalysisTK.jar \ -T VariantFiltration \ -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta \ -V /Users/mac/Desktop/NGS-/59variants.vcf \ -o /Users/mac/Desktop/NGS-/59variants.vcf \ --filterExpression "AB < 0.2 || MQ0 > 50"
INFO 11:31:49,414 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:31:49,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 11:31:49,416 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 11:31:49,417 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 11:31:49,417 HelpFormatter - [Wed Aug 26 11:31:49 WEST 2020] Executing on Mac OS X 10.15.6 x86_64
INFO 11:31:49,417 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17
INFO 11:31:49,421 HelpFormatter - Program Args: -T VariantFiltration -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta -V /Users/mac/Desktop/NGS-/59variants.vcf -o /Users/mac/Desktop/NGS-/59variants.vcf --filterExpression AB < 0.2 || MQ0 > 50
INFO 11:31:49,598 HelpFormatter - Executing as [email protected] on Mac OS X 10.15.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17.
INFO 11:31:49,599 HelpFormatter - Date/Time: 2020/08/26 11:31:49
INFO 11:31:49,599 HelpFormatter - ----------------------------------------------------------------------------------
INFO 11:31:49,600 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/Users/mac/Desktop/GenomeAnalysisTK-3.8-0-ge9d806836%204/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 11:31:50,440 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 11:31:50,440 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 11:31:50,441 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:31:50,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 11:31:50,699 GenomeAnalysisEngine - Preparing for traversal
INFO 11:31:50,701 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:31:50,702 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:31:50,702 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:31:50,702 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

ERROR --

ERROR stack trace

java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50]
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:238)
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.initialize(VariantFiltration.java:251)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
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 3.8-0-ge9d806836):

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: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50]

ERROR ------------------------------------------------------------------------------------------

how should I fix it ?!

[yunfeiguo]

Hi @elbakrifz this is more of GATK problem than a problem of SeqMule, please refer to https://cc.bingj.com/cache.aspx?q=Inconsistent+number+of+provided+filter+names+and+expressions&d=4818888926822978&mkt=en-US&setlang=en-US&w=4LBNNkST4HePYIU1e4fZ_9kSrrvxE4yZ for some info.