BUG: java.lang.IllegalStateException: The original PLs do not have enough values

StevenHartStevenHart Mayo ClinicMember

I have run HaplotypeCaller (Version=3.1-1-g07a4bf8) on 99 WGS samples and created my GVCFs. I did this in 60+ intervals to enable faster turn around time. I then merged the GVCFs with CombineGVCFs (Version=3.1-1-g07a4bf8) However, when I try to call variants with
java -jar $GATK -T GenotypeGVCFs -V WGS.gvcf.gz -o VCF/WGS.vcf.gz -R $GENOME -nt 8
it errors out complaining about PL values. The stack trace is here:

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

java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10011 but size is 10000
at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1593)
at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1530)
at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1095)
at org.broadinstitute.sting.gatk.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:183)
at org.broadinstitute.sting.gatk.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:110)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
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 original PLs do not have enough values; accessing index 10011 but size is 10000
ERROR ------------------------------------------------------------------------------------------

In the short term, is there a hidden setting I can use to skip over these, rather than completely throwing up?

Comments

  • StevenHartStevenHart Mayo ClinicMember

    Also, this is not due to the index issue. I indexed using tabix 0.2.5

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @StevenHart‌

    Hi,

    Please try running again with the latest nightly build. I think this may have been fixed.

    -Sheila

  • KurtKurt Member ✭✭✭

    I came across this error today and then reattempted to use nightly-2014-07-08-g0a593e7 first with just GenotypeGVCF. That still crashed and gave the same error. Then I tried using the nightly to recreate CombineGVCF as well as GenotypeGVCF and it still crashed.

    My actual stack trace from the nightly (it's slightly different than above);

    ERROR stack trace

    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:192)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
    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:314)
    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:107)

    cmd lines;

    $JAVA_1_7/java -jar $GATK_DIR_NIGHTLY/GenomeAnalysisTK.jar \ -T CombineGVCFs \ -R $REF_GENOME \ --variant $GVCF_LIST \ -L $CHROMOSOME \ -o $CORE_PATH/$PROJECT/GVCF/AGGREGATE/$PREFIX"."$CHROMOSOME".genome.vcf"

    and

    $JAVA_1_7/java -jar $GATK_DIR_NIGHTLY/GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R $REF_GENOME \ --variant $CORE_PATH/$PROJECT/GVCF/AGGREGATE/$PREFIX"."$CHROMOSOME".genome.vcf" \ -o $CORE_PATH/$PROJECT/TEMP/$PREFIX"."$CHROMOSOME".temp.vcf"

    This was a fairly small targeted capture (either 1 or 3 MB) with about 700 samples. It died on chromosome 21. The other chromosomes worked fine.

    I haven't come across this issue with around 700 exomes which uses the same pipeline.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hey @Kurt, sorry for the late reply. You say this still happens after rerunning the CombineGVCFs step using the nightly version? That's odd bc afaik that was a CombineGVCFs bug. If you can provide a subset of GVCF snippets that reproduces the error I'm happy to take a look.

  • KurtKurt Member ✭✭✭

    No worries @Geraldine_VdAuwera, Hopefully I can recreate this error with the subset of samples that were HapMap (that we run internally), otherwise I'm going to be hard pressed to do so otherwise.

  • KurtKurt Member ✭✭✭

    Hi @Geraldine_VdAuwera, It didn't crash when I used I used 19 HapMap samples to try an recreate the problem, but it still does crash when I try to do all 869 samples together and in the same place (to be honest, I haven't done the CombineGVCFs in batches, b/c in my hands it has performed better when I just do all the samples at once and just limit it to per chromosome, then GenotypeGVCF each chromosome and then use CombineVariants afterwards).

    In any case, I think I got the okay to share snippets from the other samples of data to you, but was asked if you could send me an email confirming that you have deleted the data after debugging. Would it be best if I uploaded the single sample GVCF files for all the samples around where it crashed within an x bp window?

    Below was the previous few entries before the stack trace in my previous run.

    `WARN 17:12:17,413 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 21:42239010 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
    WARN 17:12:17,530 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 21:42239018 has 11 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
    WARN 17:12:17,589 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 21:42239020 has 15 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
    WARN 17:12:17,857 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 21:42239022 has 18 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument

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

    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:192)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
    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:314)
    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:107)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version nightly-2014-07-08-g0a593e7):
    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 original PLs do not have enough values; accessing index 10000 but size is 10000

    `

    I looked at the GVCFs for all of the samples within a few base pairs around there and the word "yeesh" comes to mind.

    Kurt

  • KurtKurt Member ✭✭✭

    Hey @Geraldine_VdAuwera,

    I narrowed the region down. It was crashing where there was a homopolymer repeat, followed by dinucleotide repeat, followed by another dinucleotide repeat. After I removed about 130 bp from the interval file, recreated the gvcf's, combinegvcf, genotype gvcf, then everything went along swimingly with 3.1-1. I can extract that region that I removed out of the original gvcf files that were causing me problems and send them to your ftp site if you are still interested (or I can try rerunning gvcf/combine/genotypegvcf with 3.2-2 first and see if it just happens to be fixed if you think it would be worth it).

    Kurt

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @Kurt If you could please test whether the issue reproduces with 3.2 that would be super helpful, thanks. If it does then we'll take your snippet for local debugging.

  • KurtKurt Member ✭✭✭
  • KurtKurt Member ✭✭✭

    Okay @Geraldine_VdAuwera, looks like somewhere along the way b/w nightly-2014-07-08-g0a593e7 and 3.2-2 this seems to have gotten fixed. Got through everything without crashing in 3.2-2 and got calls in the region that I had to exclude for 3.1-1 to work :)

    Kurt

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Whoo, great news, thanks @Kurt :)

  • dheerajdheeraj luxembourgMember

    Hi,
    I have used GATK 3.2-2 version on 2000 exome samples. I have created gVCFs using haplotype caller and combined them in batches of 200 at chromosome level using combineGVCFs. Then I ran genotypeGVCFs using those chromosome level combinedgVCFs (without using catvariants) because of memory issues. However I have 2 issues:
    1) The same error as mentioned above in some of the files:

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

    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10011 but size is 10000
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:191)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
    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.ShardTraverser.call(ShardTraverser.java:98)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:722)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
    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 original PLs do not have enough values; accessing index 10011 but size is 10000
    ERROR ------------------------------------------------------------------------------------------

    2) Incorrect remaining runtime and percentage completed in the progress meter in all the files (even the completed files). :
    In the beginning it starts at 100%:

    INFO 05:34:32,086 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 05:34:32,086 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
    INFO 05:35:02,090 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s
    INFO 05:35:32,092 ProgressMeter - 8:11002701 0.0 60.0 s 99.2 w 45.3% 2.2 m 72.0 s
    INFO 05:36:02,093 ProgressMeter - 8:11012201 0.0 90.0 s 148.8 w 45.3% 3.3 m 108.0 s
    INFO 05:36:32,094 ProgressMeter - 8:11021801 0.0 120.0 s 198.4 w 45.3% 4.4 m 2.4 m

    It ends at 49.6%:

    INFO 16:13:14,817 ProgressMeter - 8:146364001 1.44364022E8 10.6 h 4.4 m 49.6% 21.5 h 10.8 h
    INFO 16:14:14,819 ProgressMeter - 8:146364001 1.44364022E8 10.7 h 4.4 m 49.6% 21.5 h 10.8 h
    INFO 16:15:14,820 ProgressMeter - 8:146364001 1.45364022E8 10.7 h 4.4 m 49.6% 21.5 h 10.8 h
    INFO 16:15:26,753 ProgressMeter - done 1.46364022E8 10.7 h 4.4 m 49.6% 21.5 h 10.8 h
    INFO 16:15:26,754 ProgressMeter - Total runtime 38454.67 secs, 640.91 min, 10.68 hours

  • dheerajdheeraj luxembourgMember

    If it is a bug can I just avoid the problematic regions by using -L parameter while using genotypeGVCFS and later combine them ???

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @dheeraj‌

    Hello,

    This looks like a bug that affected version 3.1. Were the files you are using generated with an older version of GATK?

    -Sheila

  • dheerajdheeraj luxembourgMember

    No they were generated by using 3.2.2 version of gatk, I was able to solve this for some of the files by just avoiding one position that was causing the problem by using -L command. But I am not sure if I can do that or not.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yes, that should be fine if you don't mind skipping that one site. I think this may be a leftover from an issue that causes individual sites to be skipped in some corner cases, which is currently being debugged.

  • Hello, I am getting this error in GATK v3.2-2-gec30cee running GenotypeGVCFs on around 1000 exomes. Most chromosomes pass, but I have four chromosomes that are crashing. I see both error messages reported earlier in this thread (index 10000 and index 10011), as below. It was mentioned that this may be left over from a particular issue.

    Any insight into the cause of this? What kind of regions will tend to trigger this?

    Thanks,
    Lee-kai

    Error message with index 10000:

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

    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:191)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
    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:314)
    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:107)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
    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 original PLs do not have enough values; accessing index 10000 but size is 10000
    ERROR ------------------------------------------------------------------------------------------

    Error message with index 10011:

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

    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10011 but size is 10000
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
    at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:191)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
    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:314)
    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:107)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
    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 original PLs do not have enough values; accessing index 10011 but size is 10000
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @leekaiinthesky
    Hi Lee-kai,

    Can you please try with the latest version of GATK and see if this still happens?

    Thanks,
    Sheila

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