Bug in HaplotypeCaller?

kohrnbkohrnb Portland State UniversityMember

I was just running haplotype caller on a pool, and it gave an error message which (if I understand the options I gave it correctly) should not occur. My command was:

nice -n 5 java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -o Vars.vcf --forceActive -ploidy 18 -I input.bam --max_alternate_alleles 2 --genotyping_mode DISCOVERY

and the error stack trace I got was:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: the combination of ploidy (18) and number of alleles (17) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator.(GenotypeLikelihoodCalculator.java:214)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators.getInstance(GenotypeLikelihoodCalculators.java:327)
at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator(InfiniteRandomMatingPopulationModel.java:145)
at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.singleSampleLikelihoods(InfiniteRandomMatingPopulationModel.java:137)
at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.calculateLikelihoods(InfiniteRandomMatingPopulationModel.java:115)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.calculateGLsForThisEvent(HaplotypeCallerGenotypingEngine.java:695)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:269)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:924)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:228)
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.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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 http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: the combination of ploidy (18) and number of alleles (17) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
ERROR ------------------------------------------------------------------------------------------

If I understand the options correctly, I told GATK to only use two possible alternates, so I'm not sure why this error message is showing up.

Incidentally, earlier I got an error message saying GATK had run out of memory with a very similar command. If necessary, I can send you my input file and reference genome. (I'm working with pooled chloroplast data for this file).

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @kohrnb
    Hi,

    I'm not sure why the -max_alternate_alleles argument is not working for you. You are correct you should not get the error message, but the argument does work for me. Can you submit a bug report? Instructions are here.

    Thanks,
    Sheila

  • kohrnbkohrnb Portland State UniversityMember

    Got it. I've uploaded the files as GATK_BugReport_kohrnb_20160407.zip; for me, the snippet produced a similar error almost instantly.

    In case it matters, I'm working on a linux server running CentOS 6.5 with 189 GB available RAM and 2 x Intel Xeon E5-2665 processors.
    Also, it seems like it might be related to the memory issue mentioned at http://gatkforums.broadinstitute.org/gatk/discussion/comment/29092/#Comment_29092 (at least, this happened when I turned off downsampling on the file in question).

    Thanks for the help,
    Brendan

    Issue · Github
    by Sheila

    Issue Number
    815
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    chandrans
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @kohrnb
    Hi Brendan,

    I just tried running HaplotypeCaller on the BAM file you uploaded, and I do not get the error message you posted. I'm not sure what is going on. But, I do get a message like this: WARN 13:19:38,366 ExactAFCalculator - this tool is currently set to genotype at most 2 alternate alleles in a given context, but the context at gi|704001763|gb|KM360047.1|:33034 has 3 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.

    This is what is supposed to happen when the tool runs into a site that has more than the max requested alternate allele.

    I used the basic HaplotypeCaller command on your files with just -ploidy 18 --max_alternate_alleles 2 --forceActive added.

    -Sheila

  • kohrnbkohrnb Portland State UniversityMember
    edited April 2016

    Hi Sheila,

    I just reran the snippet I sent you, and got the following output:

    [bkohrn@circe CallHapSNPs]$ nice -n 5 java -jar /vol/share/cruzan_lab/bioinformatics/programs/GenomeAnalysisTK.jar -T HaplotypeCaller -R /vol/share/cruzan_lab/bioinformatics/genomes/Lasbur_cp_KM360047_1_circularized.fasta -I GATK_Snippet.bam -o TestSnippetVars.vcf --forceActive -ploidy 18 --max_alternate_alleles 2 --genotyping_mode DISCOVERY
    INFO 12:25:23,605 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:25:23,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO 12:25:23,607 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 12:25:23,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 12:25:23,611 HelpFormatter - Program Args: -T HaplotypeCaller -R /vol/share/cruzan_lab/bioinformatics/genomes/Lasbur_cp_KM360047_1_circularized.fasta -I GATK_Snippet.bam -o TestSnippetVars.vcf --forceActive -ploidy 18 --max_alternate_alleles 2 --genotyping_mode DISCOVERY
    INFO 12:25:23,625 HelpFormatter - Executing as bkohrn@circe.rc.pdx.edu on Linux 2.6.32-573.22.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_99-mockbuild_2016_03_25_02_19-b00.
    INFO 12:25:23,625 HelpFormatter - Date/Time: 2016/04/26 12:25:23
    INFO 12:25:23,626 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:25:23,626 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:25:23,752 GenomeAnalysisEngine - Strictness is SILENT
    INFO 12:25:23,838 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO 12:25:23,845 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 12:25:23,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
    INFO 12:25:23,894 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
    INFO 12:25:23,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 12:25:23,970 GenomeAnalysisEngine - Done preparing for traversal
    INFO 12:25:23,970 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 12:25:23,970 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 12:25:23,971 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
    INFO 12:25:23,971 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
    INFO 12:25:24,015 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    WARN 12:25:24,016 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
    INFO 12:25:24,016 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    INFO 12:25:24,085 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
    Using AVX accelerated implementation of PairHMM
    INFO 12:25:27,942 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
    INFO 12:25:27,942 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
    WARN 12:25:33,737 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
    WARN 12:25:40,537 ExactAFCalculator - this tool is currently set to genotype at most 2 alternate alleles in a given context, but the context at gi|704001763|gb|KM360047.1|:33034 has 3 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.
    INFO 12:25:53,973 ProgressMeter - gi|704001763|gb|KM360047.1|:33536 0.0 30.0 s 49.6 w 22.2% 2.3 m 105.0 s
    INFO 12:26:23,974 ProgressMeter - gi|704001763|gb|KM360047.1|:34079 0.0 60.0 s 99.2 w 22.5% 4.4 m 3.4 m
    INFO 12:26:42,275 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.IllegalArgumentException: the combination of ploidy (18) and number of alleles (18) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator.(GenotypeLikelihoodCalculator.java:214)
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators.getInstance(GenotypeLikelihoodCalculators.java:327)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator(InfiniteRandomMatingPopulationModel.java:145)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.singleSampleLikelihoods(InfiniteRandomMatingPopulationModel.java:137)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.calculateLikelihoods(InfiniteRandomMatingPopulationModel.java:115)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.calculateGLsForThisEvent(HaplotypeCallerGenotypingEngine.java:695)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:269)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:924)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:228)
    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.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    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 http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: the combination of ploidy (18) and number of alleles (18) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
    ERROR ------------------------------------------------------------------------------------------

    If I don't set genotyping_mode (which I feel like I should be setting, since I'm trying to discover variants), I get the same error. Should I be using a different version of GATK? Or could it be an issue with the version of Java on the server? I'm running with:

    [bkohrn@circe GATK_BugReport_kohrnb_20160407]$ java -version
    java version "1.7.0_99"
    OpenJDK Runtime Environment (rhel-2.6.5.0.el6_7-x86_64 u99-b00)
    OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode)

    Thanks for the help, either way,
    Brendan

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

    @kohrnb
    Hi Brendan,

    We don't support OpenJDK. Perhaps that is the issue. Can you try to reproduce the issue with Oracle JDK?

    Thanks,
    Sheila

  • kohrnbkohrnb Portland State UniversityMember

    I can try...not sure if I can install a different version of Java on the server in question.

  • kohrnbkohrnb Portland State UniversityMember

    OK...downloaded java from Oracle, and got this output:
    [bkohrn@circe CallHapSNPs]$ ~/src/jdk1.8.0_91/bin/java -version
    java version "1.8.0_91"
    Java(TM) SE Runtime Environment (build 1.8.0_91-b14)
    Java HotSpot(TM) 64-Bit Server VM (build 25.91-b14, mixed mode)

    [bkohrn@circe CallHapSNPs]$ nice -n 5 ~/src/jdk1.8.0_91/bin/java -jar /vol/share/cruzan_lab/bioinformatics/programs/GenomeAnalysisTK.jar -T HaplotypeCaller -R /vol/share/cruzan_lab/bioinformatics/genomes/Lasbur_cp_KM360047_1_circularized
    .fasta -I /disk/scratch/Cruzan/Preproc_Test/CallHapSNPs/GATK_Snippet.bam -o TestSnippetVars.vcf --forceActive -ploidy 18 --max_alternate_alleles 2 --genotyping_mode DISCOVERY
    INFO 18:28:04,254 HelpFormatter - --------------------------------------------------------------------------------
    INFO 18:28:04,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO 18:28:04,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 18:28:04,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 18:28:04,261 HelpFormatter - Program Args: -T HaplotypeCaller -R /vol/share/cruzan_lab/bioinformatics/genomes/Lasbur_cp_KM360047_1_circularized.fasta -I /disk/scratch/Cruzan/Preproc_Test/CallHapSNPs/GATK_Snippet.bam -o TestSnippetV
    ars.vcf --forceActive -ploidy 18 --max_alternate_alleles 2 --genotyping_mode DISCOVERY
    INFO 18:28:04,271 HelpFormatter - Executing as bkohrn@circe.rc.pdx.edu on Linux 2.6.32-573.22.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14.
    INFO 18:28:04,271 HelpFormatter - Date/Time: 2016/04/28 18:28:04
    INFO 18:28:04,272 HelpFormatter - --------------------------------------------------------------------------------
    INFO 18:28:04,272 HelpFormatter - --------------------------------------------------------------------------------
    INFO 18:28:04,759 GenomeAnalysisEngine - Strictness is SILENT
    INFO 18:28:04,834 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
    INFO 18:28:04,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 18:28:04,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
    INFO 18:28:04,889 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
    INFO 18:28:04,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 18:28:04,970 GenomeAnalysisEngine - Done preparing for traversal
    INFO 18:28:04,970 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 18:28:04,970 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 18:28:04,970 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
    INFO 18:28:04,971 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
    INFO 18:28:05,008 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    WARN 18:28:05,008 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
    INFO 18:28:05,009 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
    INFO 18:28:05,051 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
    Using AVX accelerated implementation of PairHMM
    INFO 18:28:07,473 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
    INFO 18:28:07,473 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
    WARN 18:28:13,268 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
    WARN 18:28:19,883 ExactAFCalculator - this tool is currently set to genotype at most 2 alternate alleles in a given context, but the context at gi|704001763|gb|KM360047.1|:33034 has 3 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument. This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.
    INFO 18:28:34,973 ProgressMeter - gi|704001763|gb|KM360047.1|:33536 0.0 30.0 s 49.6 w 22.2% 2.3 m 105.0 s
    INFO 18:29:04,974 ProgressMeter - gi|704001763|gb|KM360047.1|:34079 0.0 60.0 s 99.2 w 22.5% 4.4 m 3.4 m
    INFO 18:29:24,338 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.IllegalArgumentException: the combination of ploidy (18) and number of alleles (18) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator.(GenotypeLikelihoodCalculator.java:214)
    at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators.getInstance(GenotypeLikelihoodCalculators.java:327)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator(InfiniteRandomMatingPopulationModel.java:145)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.singleSampleLikelihoods(InfiniteRandomMatingPopulationModel.java:137)
    at org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel.calculateLikelihoods(InfiniteRandomMatingPopulationModel.java:115)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.calculateGLsForThisEvent(HaplotypeCallerGenotypingEngine.java:695)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:269)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:924)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:228)
    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.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
    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 http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: the combination of ploidy (18) and number of alleles (18) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyze this locus
    ERROR ------------------------------------------------------------------------------------------

    I ran without the --genotyping_mode DISCOVERY option and got the same error. I then downloaded the 1.7 version, and (without --genotyping_mode), and got the error again.

    Is there a specific version of Java I should try?

    Issue · Github
    by Sheila

    Issue Number
    850
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    chandrans
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @kohrnb
    Hi Brendan,

    The current release supports Java 1.7, but if you are using the latest nightly build, you will need to use Java 1.8. Let me talk to the team and get back to you.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @kohrnb
    Hi Brendan,

    Sorry for the delay. I got the error to reproduce now (I swear it worked fine last week with no errors! :confused:). We already have people assigned to it, so hopefully the fix is in very soon. You can keep track of the bug here.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @kohrnb
    Hi Brendan,

    This has been fixed in the latest nightly build :smiley:

    -Sheila

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