Question: I'm facing a strange GATK error in one of my operations. I'm not sure what's happening here. See:

```
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.IllegalArgumentException: Permitted to write any record upstream of position 195509918, but a record at 3:195509765 was just added.
at htsjdk.variant.variantcontext.writer.SortingVariantContextWriterBase.noteCurrentRecord(SortingVariantContextWriterBase.java:161)
at htsjdk.variant.variantcontext.writer.SortingVariantContextWriter.noteCurrentRecord(SortingVariantContextWriter.java:55)
at htsjdk.variant.variantcontext.writer.SortingVariantContextWriterBase.add(SortingVariantContextWriterBase.java:128)
at edu.mssm.gatk.walkers.variantutils.AnnotateLikelyPathogenic$RetainedVariants.writeUpTo(AnnotateLikelyPathogenic.java:684)
at edu.mssm.gatk.walkers.variantutils.AnnotateLikelyPathogenic$RetainedVariants.writeUpTo(AnnotateLikelyPathogenic.java:692)
at edu.mssm.gatk.walkers.variantutils.AnnotateLikelyPathogenic.map(AnnotateLikelyPathogenic.java:324)
at edu.mssm.gatk.walkers.variantutils.AnnotateLikelyPathogenic.map(AnnotateLikelyPathogenic.java:42)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.7.2b-987-g23a99ad):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Permitted to write any record upstream of position 195509918, but a record at 3:195509765 was just added.
##### ERROR ------------------------------------------------------------------------------------------
```

Can anyone help me out here? I can provide more information once I get a direction on how to dig deeper into this.

Answer: Strange error but I think that I encountered something similar... somewhere!

The first place that I'd look is at the genome index. For example, did you create the sequence dictionary yourself using your own version of java and Picard, or download it from somewhere else?