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GATK exit code -9

I tried to run BQSR but got an exit code -9 with no further explanation. What does it mean?
The error code:

Executing ' java -Xmx220g -XX:ParallelGCThreads=4 -XX:+UseG1GC -XX:ConcGCThreads=1 -jar /usr/local/apps/GATK/3.8-0/GenomeAnalysisTK.jar -T BaseRecalibrator -R /data/nextgen/Xiaopeng/DCEG/ref/human_g1k_v37_decoy.fasta -I /data/DCEGTumorWGS/BAMs/SN0101262/vc_benchmark/precisionFDA_maurizio_bam/6_10_90_HQ_paired_dedup_properly_paired_nophix.bam -knownSites /data/nextgen/Xiaopeng/DCEG/ref/dbsnp_138.b37.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/Mills_and_1000G_gold_standard.indels.hg19.nochr.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/1000G_phase1.indels.hg19.nochr.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/cosmic82vcf/CosmicCodingMuts.vcf.gz -knownSites /data/nextgen/Xiaopeng/DCEG/ref/cosmic82vcf/CosmicNonCodingVariants.vcf.gz -o ./cosmi82/6_10_90_HQ_paired_dedup_properly_paired_nophix.recal_cosmi82.table --use_jdk_inflater --use_jdk_deflater '
INFO 10:53:47,015 HelpFormatter - ----------------------------------------------------------------------------------
INFO 10:53:47,019 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 10:53:47,019 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 10:53:47,020 HelpFormatter - For support and documentation go to
INFO 10:53:47,020 HelpFormatter - [Thu Mar 29 10:53:46 EDT 2018] Executing on Linux 2.6.32-642.3.1.el6.x86_64 amd64
INFO 10:53:47,021 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_11-b12
INFO 10:53:47,025 HelpFormatter - Program Args: -T BaseRecalibrator -R /data/nextgen/Xiaopeng/DCEG/ref/human_g1k_v37_decoy.fasta -I /data/DCEGTumorWGS/BAMs/SN0101262/vc_benchmark/precisionFDA_maurizio_bam/6_10_90_HQ_paired_dedup_properly_paired_nophix.bam -knownSites /data/nextgen/Xiaopeng/DCEG/ref/dbsnp_138.b37.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/Mills_and_1000G_gold_standard.indels.hg19.nochr.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/1000G_phase1.indels.hg19.nochr.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/cosmic82vcf/CosmicCodingMuts.vcf.gz -knownSites /data/nextgen/Xiaopeng/DCEG/ref/cosmic82vcf/CosmicNonCodingVariants.vcf.gz -o ./cosmi82/6_10_90_HQ_paired_dedup_properly_paired_nophix.recal_cosmi82.table --use_jdk_inflater --use_jdk_deflater
INFO 10:53:47,029 HelpFormatter - Executing as [email protected] on Linux 2.6.32-642.3.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_11-b12.
INFO 10:53:47,030 HelpFormatter - Date/Time: 2018/03/29 10:53:47
INFO 10:53:47,030 HelpFormatter - ----------------------------------------------------------------------------------
INFO 10:53:47,030 HelpFormatter - ----------------------------------------------------------------------------------
INFO 10:53:47,063 GenomeAnalysisEngine - Deflater: JdkDeflater
INFO 10:53:47,063 GenomeAnalysisEngine - Inflater: JdkInflater
INFO 10:53:47,064 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:53:47,224 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 10:53:47,233 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 10:53:47,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
GATK finished (exit code -9)



  • Please some GATK experts look at and answer this one?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I am not sure what exit code -9 means. Are you running this as a separate command in your terminal? If not, can you try it? Can you also try validating your input BAM file with ValidateSamFile?


  • I am not sure what do you mean by run as separate, but here is the command I used:
    java -Xmx220g -XX:ParallelGCThreads=4 -XX:+UseG1GC -XX:ConcGCThreads=1 -jar /GATK/3.8-0/GenomeAnalysisTK.jar -T BaseRecalibrator -R /ref/human_g1k_v37_decoy.fasta -I /bam/5_20_80_HQ_paired_dedup_properly_paired_nophix.bam -knownSites /data/ref/dbsnp_138.b37.vcf -knownSites /data/ref/Mills_and_1000G_gold_standard.indels.hg19.nochr.vcf -knownSites /data/ref/1000G_phase1.indels.hg19.nochr.vcf -knownSites /data/nextgen/Xiaopeng/DCEG/ref/cosmic82vcf/CosmicCodingMuts.vcf.gz -knownSites /data/ref/cosmic82vcf/CosmicNonCodingVariants.vcf.gz -o ./cosmi82/5_20_80_HQ_paired_dedup_properly_paired_nophix.recal_cosmi82.table --use_jdk_inflater --use_jdk_deflater

    I used the same bam files for bqsr without COSMIC successfully, so it seems the problem is the COSMIC file, but I used this COSMIC file in Mutect successfully, so I think that the problem is COSMIC used in BQSR.

  • I posted thee error log in my original post,but I could not find any clue in it. Did you see anything wrong in it?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin



    Interesting. So, yes, the issue is with Cosmic. We don't recommend using it in BQSR; we only recommend using germline known variants.

    Can you try running ValidateVariants on the Cosmic VCF?


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