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Null pointer exception using GATK2 at chr19 for mouse genome
I'm doing tumor normal somatic variant calling using ** MuTect2 (gatk v188.8.131.52)**. I have used mm10 reference genome for mapping and I have tried following the general best practices of GATK and Mutect2.
But for some reason the variant calling breaks at chr19 and reports a null pointer exception. This happens to all my samples.
The command I have used for running MuTect2 is as below:
gatk Mutect2 \ -R $ref \ -I $BAMs/3_MOO111A3_S8_001.markdup.realigned.bam \ -I $BAMs/4_MOO111A4_S11_001.markdup.realigned.bam \ -tumor 3_MOO111A3_S8_001 \ -normal 4_MOO111A4_S11_001 \ -O $out/3_4_unfiltered.vcf.gz \ -bamout $out/3_4_tumor_normal.bam
The error I get is as follows:
02:04:08.372 INFO ProgressMeter - chr19:61211311 984.9 4994610 5071.4 02:04:19.192 INFO ProgressMeter - chr19:61266818 985.0 4994840 5070.7 02:04:27.335 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 39.543984247000004 02:04:27.335 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 15107.717470987001 02:04:27.336 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 14077.45 sec INFO 2019-07-11 02:04:28 SortingCollection Creating merging iterator from 34 files 02:05:08.531 INFO Mutect2 - Shutting down engine [July 11, 2019 2:05:08 AM EDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 985.91 minutes. Runtime.totalMemory()=2113929216 java.lang.NullPointerException at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:98) at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:49) at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$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.<init>(PushToPullIterator.java:37) at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.<init>(ReadsDownsamplingIterator.java:21) at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:149) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(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)
I have tried reading other posts with Null pointers exception, but could not find a solution for my issue.
I also validate my bam using ValidateSam from picard as per one of the answers. There were no issues/errors with my bam files.