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Gatk Mutect2 4.1.2.0 got errors

I run Gatk 4.1.2.0 mutect 2. I look at its results. Mutect2 is done, but final errors:
00:42:00.798 INFO ProgressMeter - Y:27720454 851.5 11556090 13571.2
00:42:10.860 INFO ProgressMeter - Y:59021204 851.7 11660610 13691.2
00:42:21.010 INFO ProgressMeter - GL000231.1:14228 851.9 11662230 13690.4
00:42:31.291 INFO ProgressMeter - GL000234.1:39486 852.0 11664530 13690.4
00:42:41.370 INFO ProgressMeter - GL000241.1:36592 852.2 11665440 13688.7
00:42:51.697 INFO ProgressMeter - GL000198.1:62441 852.4 11666930 13687.7
00:43:02.221 INFO ProgressMeter - GL000214.1:132192 852.5 11669460 13687.9
00:43:12.363 INFO ProgressMeter - GL000218.1:43586 852.7 11670870 13686.8
00:43:24.288 INFO ProgressMeter - GL000220.1:119449 852.9 11672080 13685.0
00:43:38.369 INFO ProgressMeter - GL000220.1:123353 853.1 11672110 13681.3
00:43:49.405 INFO ProgressMeter - GL000220.1:128631 853.3 11672150 13678.4
00:44:00.080 INFO ProgressMeter - GL000220.1:137802 853.5 11672210 13675.6
00:44:10.302 INFO ProgressMeter - GL000220.1:149184 853.7 11672290 13673.0
00:44:20.376 INFO ProgressMeter - GL000205.1:18186 853.8 11676250 13674.9
00:44:31.151 INFO ProgressMeter - GL000219.1:59083 854.0 11677410 13673.4
00:44:41.158 INFO ProgressMeter - GL000195.1:14690 854.2 11679590 13673.3
00:44:51.954 INFO ProgressMeter - GL000195.1:139748 854.4 11680370 13671.3
00:45:02.028 INFO ProgressMeter - GL000194.1:5110 854.5 11683480 13672.3
00:45:12.112 INFO ProgressMeter - GL000225.1:23759 854.7 11684410 13670.7
00:45:22.726 INFO ProgressMeter - GL000225.1:65740 854.9 11684710 13668.2
00:45:32.857 INFO ProgressMeter - GL000192.1:118283 855.1 11685900 13666.9
00:45:37.277 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 80.57987107800001
00:45:37.278 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 9363.937072385
00:45:37.278 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 3052.87 sec
00:45:37.279 INFO Mutect2 - Shutting down engine
[May 16, 2019 12:45:37 AM CDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 855.17 minutes.
Runtime.totalMemory()=861405184
java.lang.NullPointerException
at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:98)
at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:49)
at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:42)
at org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.next(ReadTransformingIterator.java:14)
at org.broadinstitute.hellbender.utils.iterators.PushToPullIterator.fillCache(PushToPullIterator.java:72)
at org.broadinstitute.hellbender.utils.iterators.PushToPullIterator.advanceToNextElement(PushToPullIterator.java:58)
at org.broadinstitute.hellbender.utils.iterators.PushToPullIterator.(PushToPullIterator.java:37)
at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.(ReadsDownsamplingIterator.java:21)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:149)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.(AssemblyRegionIterator.java:109)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:296)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:281)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
(END)

Please help fix. Thanks.

Answers

  • AdelaideRAdelaideR Member admin

    It would be helpful to see the command, but you can disable the filters that may be leading to this output.

    There is a warning that this may cause problems:

    --disable-tool-default-read-filters / -disable-tool-default-read-filters Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)

    There is more information about how to run Mutect2 here

  • gatksungatksun Member

    Hi AdelaideR,
    When I add --disable-tool-default-read-filters, gatk stop immediately,


    15:48:55.844 INFO Mutect2 - HTSJDK Version: 2.19.0
    15:48:55.844 INFO Mutect2 - Picard Version: 2.19.0
    15:48:55.844 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    15:48:55.844 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    15:48:55.844 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    15:48:55.844 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    15:48:55.844 INFO Mutect2 - Deflater: IntelDeflater
    15:48:55.844 INFO Mutect2 - Inflater: IntelInflater
    15:48:55.844 INFO Mutect2 - GCS max retries/reopens: 20
    15:48:55.844 INFO Mutect2 - Requester pays: disabled
    15:48:55.844 INFO Mutect2 - Initializing engine
    15:48:56.277 INFO Mutect2 - Done initializing engine
    15:48:56.295 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/rsrch2/iacs/apps/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
    15:48:56.315 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/rsrch2/iacs/apps/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
    15:48:56.362 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
    15:48:56.363 INFO IntelPairHmm - Available threads: 16
    15:48:56.363 INFO IntelPairHmm - Requested threads: 4
    15:48:56.363 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
    15:48:56.414 INFO ProgressMeter - Starting traversal
    15:48:56.414 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
    15:48:56.626 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
    15:48:56.626 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
    15:48:56.627 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
    15:48:56.628 INFO Mutect2 - Shutting down engine
    [May 17, 2019 3:48:56 PM CDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.04 minutes.
    Runtime.totalMemory()=1027604480
    java.lang.NullPointerException
    at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.readStartsAtCurrentPosition(ReadStateManager.java:132)
    at org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.collectPendingReads(ReadStateManager.java:159)
    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:296)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:281)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @gatksun The null pointer exception is occurring when the code looks up a contig in the reference sequence dictionary. Given that this is happening on a weird contig GL000192.1, my best guess is that your bam has a few reads mapped to alt and/or decoy contigs that are missing from your reference. You could omit these contigs from your interval list or try to find a reference whose sequence dictionary matches your bam's.

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