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ComparableSamRecordIterator related error when running Mutect2

:) Hello GATK team,

I'm getting the error pasted below when running Mutect2 (gatk 4.0.10.0). My bam files (normal and tumour) pass the validation run as:

```
gatk ValidateSamFile -I aligned.sorted.bam
```

with the exception of the header version which I don't know wether is relevant to Mutect2

```
ERROR: Header version: 1.6 does not match any of the acceptable versions: 1.0, 1.3, 1.4, 1.5
```

This the full Mutect2 error message. Any help to get Mutect2 running will be appreciated.

Thanks so much
Jorge


```
java.lang.NullPointerException
at htsjdk.samtools.ComparableSamRecordIterator.compareTo(ComparableSamRecordIterator.java:68)
at htsjdk.samtools.ComparableSamRecordIterator.compareTo(ComparableSamRecordIterator.java:36)
at java.util.PriorityQueue.siftUpComparable(PriorityQueue.java:657)
at java.util.PriorityQueue.siftUp(PriorityQueue.java:648)
at java.util.PriorityQueue.offer(PriorityQueue.java:345)
at htsjdk.samtools.MergingSamRecordIterator.addIfNotEmpty(MergingSamRecordIterator.java:162)
at htsjdk.samtools.MergingSamRecordIterator.<init>(MergingSamRecordIterator.java:95)
at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:421)
at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:330)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
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: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)
```
Tagged:

Best Answer

  • jorgezjorgez
    Accepted Answer
    :)
    Hi,

    I'll answer to myself.

    The error was caused by the header version ( 1.6) not matching any of the acceptable versions (1.0, 1.3, 1.4, 1.5).

    This seem be fixed by adding the HD string when mapping with bwa mem like this:

    ```
    bwa mem -H '@HD\\tVN:1.5\\tGO:none\\tSO:coordinate'
    ````

    Jorge

Answers

  • jorgezjorgez Member
    Accepted Answer
    :)
    Hi,

    I'll answer to myself.

    The error was caused by the header version ( 1.6) not matching any of the acceptable versions (1.0, 1.3, 1.4, 1.5).

    This seem be fixed by adding the HD string when mapping with bwa mem like this:

    ```
    bwa mem -H '@HD\\tVN:1.5\\tGO:none\\tSO:coordinate'
    ````

    Jorge
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