Error in PalindromeArtifactClipReadTransformer

[meganshand]

Bug Report

Affected tool(s) or class(es)

Mutect2

Affected version(s)

• Latest public release version [version?]
• Latest master branch as of 7/18/18

Description

When running Mutect yesterday on Mitochondrial data I got the following error:

java.lang.IllegalArgumentException: Invalid interval. Contig:chrM start:-4 end:65

	at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:728)
	at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61)
	at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:37)
	at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:86)
	at org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.apply(PalindromeArtifactClipReadTransformer.java:48)
	at org.broadinstitute.hellbender.transformers.ReadTransformer.lambda$andThen$f85d1091$1(ReadTransformer.java:20)
	at org.broadinstitute.hellbender.transformers.ReadTransformer$$Lambda$107/1786040872.apply(Unknown Source)
	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.downsampling.ReadsDownsamplingIterator.fillDownsampledReadsCache(ReadsDownsamplingIterator.java:69)
	at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.advanceToNextRead(ReadsDownsamplingIterator.java:55)
	at org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.<init>(ReadsDownsamplingIterator.java:34)
	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:282)
	at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:993)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.instanceMain(Main.java:146)
	at org.broadinstitute.hellbender.Main.instanceMain(Main.java:187)
	at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:32)
	at org.broadinstitute.hellbender.utils.test.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:97)
	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2IntegrationTest.testTumorNormal(Mutect2IntegrationTest.java:237)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:108)
	at org.testng.internal.Invoker.invokeMethod(Invoker.java:661)
	at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:869)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1193)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
	at org.testng.TestRunner.privateRun(TestRunner.java:744)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:380)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:375)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:340)
	at org.testng.SuiteRunner.run(SuiteRunner.java:289)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1301)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1226)
	at org.testng.TestNG.runSuites(TestNG.java:1144)
	at org.testng.TestNG.run(TestNG.java:1115)
	at org.testng.IDEARemoteTestNG.run(IDEARemoteTestNG.java:72)
	at org.testng.RemoteTestNGStarter.main(RemoteTestNGStarter.java:123)

Steps to reproduce

These are the arguments I used (the input bam is on the file system):

final String[] args = {
                "-I", "/humgen/gsa-hpprojects/dev/mshand/SpecOps/Mitochondria/Filtering/IGV/198489_vs_811158/sorted.mt.1.bam",
                "-" + M2ArgumentCollection.TUMOR_SAMPLE_SHORT_NAME, "198489",
                "-R", "/humgen/gsa-hpprojects/dev/mshand/SpecOps/Mitochondria/MitochondriaOnlyFastas/Homo_sapiens_assembly38.mt_only.fasta",
                "-O", outputVcf.getAbsolutePath(),
                "--max-reads-per-alignment-start", "0",
                "-default-af", "0",
                "--initial-tumor-lod", "0",
                "--tumor-lod-to-emit", "0",
                "--min-pruning", "10",
                "--annotation", "StrandBiasBySample",
                //"--ignore-itr-artifacts", "true",
        };

I tried it with and without --ignore-itr-artifacts but got the same error both times.

@davidbenjamin Any idea if this is an easy fix?

[davidbenjamin]

@meganshand Probably. I will try to fix it today. First, could you tell me if there's anything special about mitochondria being circular that I should know i.e. is there some equivalence between -4 and 16566 or whatever? If so, my error is venial; if not, I'm just a bozo.

[meganshand]

The fact that it's circular means that there are reads and bases right up against the edge of the contig and often have soft clips that extend beyond the contig. So it looks a bit like this:

So yes, circular means it's probably throwing in a weird edge case.