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Combine GVCF generate java.lang.NullPointerException

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Yangyxt

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.1


b) Exact command used:

time "$gatk" CombineGVCFs \
-G StandardAnnotation \
-G AS_StandardAnnotation \
-R "$ref_gen"/ucsc.hg19.fasta \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200272.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200273.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200274.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200313.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200314.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200315.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/PID20-006.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/PID20-007.HC.g.vcf.gz \
-V /paedwy/disk1/yangyxt/wes/backup_gvcfs/all_wes_samples.g.vcf \
-O /paedwy/disk1/yangyxt/wes/backup_gvcfs/all_wes_samples_plus_${sample_batch}.g.vcf.gz && echo "Combine_gvcfs done"

c) Entire error log:

12:01:36.798 WARN GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default
12:01:36.824 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/yangyxt/software/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 24, 2020 12:01:37 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:01:37.108 INFO CombineGVCFs - ------------------------------------------------------------
12:01:37.108 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.8.1
12:01:37.108 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
12:01:37.108 INFO CombineGVCFs - Executing as yangyxt@paedyl01 on Linux v3.10.0-1062.18.1.el7.x86_64 amd64
12:01:37.108 INFO CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12
12:01:37.108 INFO CombineGVCFs - Start Date/Time: August 24, 2020 12:01:36 PM HKT
12:01:37.108 INFO CombineGVCFs - ------------------------------------------------------------
12:01:37.108 INFO CombineGVCFs - ------------------------------------------------------------
12:01:37.109 INFO CombineGVCFs - HTSJDK Version: 2.23.0
12:01:37.109 INFO CombineGVCFs - Picard Version: 2.22.8
12:01:37.109 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:01:37.109 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:01:37.109 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:01:37.109 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:01:37.109 INFO CombineGVCFs - Deflater: IntelDeflater
12:01:37.109 INFO CombineGVCFs - Inflater: IntelInflater
12:01:37.109 INFO CombineGVCFs - GCS max retries/reopens: 20
12:01:37.109 INFO CombineGVCFs - Requester pays: disabled
12:01:37.109 INFO CombineGVCFs - Initializing engine
12:01:37.474 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200272.HC.g.vcf.gz
12:01:37.645 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200273.HC.g.vcf.gz
12:01:37.770 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200274.HC.g.vcf.gz
12:01:37.889 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200313.HC.g.vcf.gz
12:01:37.955 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200314.HC.g.vcf.gz
12:01:38.062 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/A200315.HC.g.vcf.gz
12:01:38.184 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/PID20-006.HC.g.vcf.gz
12:01:38.311 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/8_samples_20200819/gvcfs/PID20-007.HC.g.vcf.gz
12:01:38.417 INFO FeatureManager - Using codec VCFCodec to read file file:///paedwy/disk1/yangyxt/wes/backup_gvcfs/all_wes_samples.g.vcf
12:01:49.097 INFO CombineGVCFs - Done initializing engine
12:01:49.113 INFO ProgressMeter - Starting traversal
12:01:49.113 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
12:01:49.492 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location chrM:63 the annotation MLEAC=[2, 0] was not a numerical value and was ignored
12:01:49.505 INFO CombineGVCFs - Shutting down engine
[August 24, 2020 12:01:49 PM HKT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=6277824512
java.lang.NullPointerException
at org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils.encode(StrandBiasUtils.java:52)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils.makeRawAnnotationString(StrandBiasUtils.java:46)
at org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest.combineRawData(AS_StrandBiasTest.java:115)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.combineAnnotations(VariantAnnotatorEngine.java:210)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.mergeAttributes(ReferenceConfidenceVariantContextMerger.java:318)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:142)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:403)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:217)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:162)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:131)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:106)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:120)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:163)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /home/yangyxt/software/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?

0

6 comments

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  • Avatar
    Bhanu Gandham

    Hi Yangyxt

    Thank you for reporting this issue. This looks like a bug and we have created a github issue here. You can use that link to track the progress that the team makes to solve the issue.

    A workaround that you can use  in the meantime is to exclude the StrandBias annotation. You can do that using this argument: "--annotations-to-exclude StrandBiasBySample"

    0
    Comment actions Permalink
  • Avatar
    Yangyxt

    Dear Gandham,

    Thank you for your response! Can I ask what effect will I get to exclude this StrandBiasBySample annotation?

    0
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  • Avatar
    Genevieve Brandt (she/her)

    Hi Yangyxt, I just spoke with my team about that workaround. It is leaving out the StrandBias annotation from your output, which may not be the best option.

    A better option would be to use an older version of CombineGVCFs before this bug existed. I would try 4.1.4.1 and see if that works.

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  • Avatar
    Genevieve Brandt (she/her)

    Yangyxt we are looking at recreating this issue. Are there any 3 VCFs that replicate this problem? Please upload those 3 as a bug report as well as a link to the reference you are using. Let me know when you have done this and what you have named the folder. 

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  • Avatar
    Genevieve Brandt (she/her)
    • Edited

    Yangyxt do you have an update about sending those files so we can check the issue on our end?

    Could you also try this command with GATK 4.1.6.0 and see if the issue persists? We are working to find the specific issue.

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    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    This issue has been resolved: https://github.com/broadinstitute/gatk/issues/6766

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