MuTect generating empty VCF file

I'm new to MuTect, but I keep getting an empty VCF file when I run. I'm working with fairly low variant frequencies (<5%), but I have a synthetic WT "normal" as my tumor/normal pair, so the background is low. Using other methods, I've identified 10-15 mutations that are >10-fold higher in my sample than in my synthetic normal, but I can't replicate the results with MuTect Here's the output:

03:39:59.750 INFO IntelPairHmm - Available threads: 8
03:39:59.750 INFO IntelPairHmm - Requested threads: 4
03:39:59.751 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
03:39:59.838 INFO ProgressMeter - Starting traversal
03:39:59.839 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
03:40:09.854 INFO ProgressMeter - 1:37436701 0.2 124790 748740.0
03:40:19.839 INFO ProgressMeter - 1:88544701 0.3 295150 885450.0
03:40:29.839 INFO ProgressMeter - 1:140798701 0.5 469330 938660.0
03:40:39.839 INFO ProgressMeter - 1:194402701 0.7 648010 972015.0
03:40:49.839 INFO ProgressMeter - 1:247406701 0.8 824690 989628.0
03:40:59.839 INFO ProgressMeter - 2:54147901 1.0 1011330 1011330.0
03:41:09.839 INFO ProgressMeter - 2:112905901 1.2 1207190 1034734.3
03:41:19.839 INFO ProgressMeter - 2:171579901 1.3 1402770 1052077.5
03:41:29.839 INFO ProgressMeter - 2:230160901 1.5 1598040 1065360.0
03:41:34.539 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
03:41:34.540 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
03:41:34.540 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
03:41:34.541 INFO Mutect2 - Shutting down engine
[January 18, 2019 3:41:34 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 1.61 minutes.
Runtime.totalMemory()=1574961152
java.lang.IllegalStateException: Offered read with sample name null to SamplePartitioner but this sample wasn't provided as one of possible samples at construction
at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:749)
at org.broadinstitute.hellbender.utils.locusiterator.SamplePartitioner.submitRead(SamplePartitioner.java:86)
at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.submitRead(ReadStateManager.java:188)
at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:160)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:315)
at org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.hasNext(LocusIteratorByState.java:252)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.advanceAlignmentContext(IntervalAlignmentContextIterator.java:104)
at org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.(IntervalAlignmentContextIterator.java:45)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.(AssemblyRegionIterator.java:117)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:282)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
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)
[email protected]:/mnt/c/gatk-4.0.12.0$ java.lang.IllegalStateException: Offered read with sample name null to SamplePartitioner but this sample wasn't provided as one of possible samples at construction^C
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Answers

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @dcraig01

    I would check that your sample names match your inputs.

    There is an error that says:

     Offered read with sample name null to SamplePartitioner but this sample wasn't provided as one of possible samples at construction
    

    It may be a simple typo in your sample list.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @dcraig01, I received input from the GATK team that the absence of Read Groups can cause this to happen as well.

    The "null" in the message "Offered read with sample name null" means that the read doesn't have a read group, which is forbidden by the GATK. Fortunately, there is a Picard tool AddOrReplaceReadGroups that can fix this.

    Mutect2 output an empty VCF file because it was not able to proceed without the read groups.

    You can find out more about how to use AddOrReplaceReadGroups here

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