GATK AnnotateLikelyPathogenic strange error

Question

[Ram]

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 1

[Kevin Blighe]

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?

[Ram]

It's a standard file used across the organization. I've used it multiple times, but yeah, the VCF file was created elsewhere so maybe I should get the genome index from the other org?

[Kevin Blighe]

Using a shared system? - that can always lead to compatibility issues! If you could test it on your laptop/Mac, that would also work, just to see if it is indeed the problem.

[Ram]

I would if I could. It works fine when the same samples are split into smaller pools, and there are way too many (1000+) to run on my local computer. I think this might have happened because my java temp directory ran out of space. I cleared that up and tried a different technique and got the results, I'll try again later using the old technique once I get some time.

[Kevin Blighe]

Good call. I had also wondered if it was a space or RAM issue, but wasn't sure to what extent.

[Ram]

It's not a RAM or space issue - I tried the old route once again, and it gave me a whole new error on features being out of order.

This could be because of the variety of tools and GATK versions used along the pipeline - the VCF was generated using GATK 3.6+, and I'm trying to process it using GATK 2.7 (which is what's used in my org's super-outdated pipeline). Anyway, it's done and I'm going to leave this here.

[WouterDeCoster]

It's not a RAM issue

That's exactly what a Ram would say.

[Kevin Blighe]

You made me laugh! - a rare event!

[Ram]

I have a theory: any sufficiently populated online forum is (at times) indistinguishable from reddit.

[WouterDeCoster]

It's Friday afternoon in my timezone if that explains anything.

[Ram]

See? "It's Friday 5 PM somewhere"

[Kevin Blighe]

Only 10:15AM here... I'm abroad working on a project...