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GATK ERROR MESSAGE: 38 HaplotipeCaller

Hello everyone,

I´m using HaplotypeCaller program in whole sheep genome.

The next paragraph is the command used for all 158 samples. We use nodes of 16 cores (-ntc 16) and 28 Gb of memory RAM.

Could you tell me what the next mistake might be?
thank you in advance
-------------------------------------------------------------------------------------------------------------------------------------------------------------

ERROR --
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 38
at org.broadinstitute.gatk.tools.walkers.annotator.BaseQualityRankSumTest.getElementForRead(BaseQualityRankSumTest.java:96)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.getElementForRead(RankSumTest.java:209)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.fillQualsFromLikelihoodMap(RankSumTest.java:187)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.annotate(RankSumTest.java:104)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:315)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:260)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.annotateCall(HaplotypeCallerGenotypingEngine.java:328)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:290)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:970)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:252)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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: 38

##### ERROR ------------------------------------------------------------------------------------------

-------------------------------------------------------------------------------------------------------------------------------------------------------------

Best Answer

Answers

  • SkyWarriorSkyWarrior TurkeyMember
    Accepted Answer

    16 threads might be depleting possible sources to process. It is better you try with nct no higher than 4 or just try single threaded.

  • Hi all,
    I am trying to run Realignment stage from SNP calling for whole genome sequencing and getting the following error massage. any idea what this might be?
    thanks!
    Mostafa

    Code i run:
    java -jar /home/m.rafiepour222/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomic.fa -T RealignerTargetCreator –o /home/m.rafiepour222/SRR3112430/SRR3112430indels_Realigner.intervals -I /home/m.rafiepour222/SRR3112430/SRR3112430.sort.rmdup.bam

    My error massage:
    INFO 20:15:55,513 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 20:15:55,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
    INFO 20:15:55,518 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 20:15:55,518 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 20:15:55,519 HelpFormatter - [Sun Feb 04 20:15:55 IRST 2018] Executing on Linux 2.6.32-431.el6.x86_64 amd64
    INFO 20:15:55,521 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b11
    INFO 20:15:55,527 HelpFormatter - Program Args: -R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomic.fa -T RealignerTargetCreator -o /home/m.rafiepour222/SRR3112430/SRR3112430indels_Realigner.intervals -I /home/m.rafiepour222/SRR3112430/SRR3112430.sort.rmdup.bam
    INFO 20:15:55,536 HelpFormatter - Executing as m.rafiepour222@abrii2 on Linux 2.6.32-431.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b11.
    INFO 20:15:55,537 HelpFormatter - Date/Time: 2018/02/04 20:15:55
    INFO 20:15:55,537 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 20:15:55,537 HelpFormatter - ----------------------------------------------------------------------------------
    ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/home/m.rafiepour222/GenomeAnalysisTK-3.8-0-ge9d806836/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 20:15:55,780 GenomeAnalysisEngine - Deflater: IntelDeflater
    INFO 20:15:55,783 GenomeAnalysisEngine - Inflater: IntelInflater
    INFO 20:15:55,784 GenomeAnalysisEngine - Strictness is SILENT
    INFO 20:33:00,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 20:33:00,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 20:33:03,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 3.33
    INFO 20:50:24,247 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 21:07:31,116 GenomeAnalysisEngine - Done preparing for traversal
    INFO 21:07:31,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 21:07:31,119 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 21:07:31,119 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions https://software.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@719bb60d appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 62. Please see https://software.broadinstitute.org/gatk/documentation/article?id=6470 for more details and options related to this error.
    ERROR ------------------------------------------------------------------------------------------
  • SkyWarriorSkyWarrior TurkeyMember

    this tells you the exact story

    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@719bb60d appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 62. Please see

    How did you generate the bam file? What is the sequencing technology?

  • for generate bam file code i use:
    samtools view -b -S -o SRR3112430.bam SRR3112430.sam
    and sequencing technology is whole genome sequencing

  • I have another problem and that's it, i do not have the VCF file of the reference genome for stage Realignment.

  • Thank you very much SkyWarrior.
    I'll try it even though the time will increase a lot, I hope it ends soon and I can reflect the result in a commentary.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited February 8

    @m_rafiepour222
    Hi,

    Did this article in the error message help you?

    If you do not have a known sites VCF file, you can still run Indel Realignment step without it, but it will take longer. If you are using HaplotypeCaller or Mutect2, you do not need to run that step. Have a look at this blog post.

    -Sheila

  • Hi Sheila, many thanks for your reply,

    yes i using HaplotypeCaller and ignored the indel realignment step. But I have a problem in the HaplotypeCaller Step for Whole Genome Sequencing Data. after run this step i getting the following error massage (In the attached image).Due to two errors created (in the image), the run step begins and remains in this position for more than two days without having an output? any idea what this might be?

    Code i run:

    java –Xmx64g -jar /home/m.rafiepour222/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomic.fa -T HaplotypeCaller -I /home/m.rafiepour222/SRR3112417/SRR3112417.sort.rmdup.bam -o /home/m.rafiepour222/SRR3112417/SRR3112417.raw.snps.indels.g.vcf

    Best Regard

    Mostafa

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @m_rafiepour222
    Hi,

    Yep, that was a bug in 3.8 that is fixed in later versions. Have a look at this thread. Is it possible to upgrade to version 4? If not, 3.8-1 is not available in the downloads right now, but I have asked the team to add it.

    -Sheila

  • Hi Sheila, many thanks for guidance. Ok good, I'm waiting for you to send me the download link for 3.8-1.
    It's worth mentioning that I used the latest version (gatk-4.0.1.1 & gatk-4.0.1.2), but I've gotten the error again. But not similar the shared error.

    Best regard
    mostafa

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @m_rafiepour222
    Hi Mostafa,

    Yes, hopefully the download is available soon. But, are you saying you got the same error in GATK4? Can you post the exact command you ran and log output from GATK4?

    Thanks,
    Sheila

  • edited February 15

    Hi Sheila,

    Yes Sure,

    Code i use:

    java -jar /home/m.rafiepour222/gatk-4.0.1.2/gatk-pack age-4.0.1.2-local.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomi c.fa -T HaplotypeCaller -I /home/m.rafiepour222/SRR3112430/SRR3112430.sort.r mdup.bam -o /home/m.rafiepour222/SRR3112430/SRR3112430.raw.snps.indels.gvcf

    and my error:

    Post edited by m_rafiepour222 on
  • edited February 15

    @m_rafiepour222 said:
    Hi Sheila,

    Yes Sure,

    Code i use:

    java -jar /home/m.rafiepour222/gatk-4.0.1.2/gatk-pack age-4.0.1.2-local.jar –R /home/m.rafiepour222/GCF_000298355.1_BosGru_v2.0_genomi c.fa -T HaplotypeCaller -I /home/m.rafiepour222/SRR3112430/SRR3112430.sort.r mdup.bam -o /home/m.rafiepour222/SRR3112430/SRR3112430.raw.snps.indels.gvcf

    and my error:


    Post edited by m_rafiepour222 on
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @m_rafiepour222
    Hi Mostafa,

    Ah, yes, the commands have changed slightly in GATK4. Have a look at the tool doc. The -T is gone :smile:

    Also, best to upgrade to GATK4, but 3.8-1 is now available on the downloads page.

    -Sheila

  • Hi Sheila,

    many thanks for your reply, But on the download page is the only GATK-4.0.1.2 version for download??

    Can not find the link to download for 3.8-1??

    Best Regard

    mostafa

  • Hi Sheila,

    I found the 3.8-1 on the download page.

    I'm running my code and I think the error has already been resolved ?? Is my guess right?
    See the photo in the attachment.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @m_rafiepour222
    Hi Mostafa,

    Yep, looks like it is running fine now :smile:

    -Sheila

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