GATK CombineGVCFs error

Question

[Kat_Werner]

Hello!

I'm attempting to combine a few individual vcfs using GATK combineGVCFs argument and my GATK failed to finish because of an error. I need help figuring out what the error is and how to fix it! Thank you all so much. A portion of the output from it along with the error is below:

18:13:12.791 INFO  ProgressMeter - scaffold-ma2:200878361            230.0             604819000        2629457.9
18:13:22.805 INFO  ProgressMeter - scaffold-ma2:201421598            230.2             605450000        2630292.6
18:13:32.814 INFO  ProgressMeter - scaffold-ma2:202022265            230.4             606112000        2631261.7
18:13:42.823 INFO  ProgressMeter - scaffold-ma2:202622885            230.5             606780000        2632255.3
18:13:52.834 INFO  ProgressMeter - scaffold-ma2:203206346            230.7             607411000        2633086.8
18:14:02.843 INFO  ProgressMeter - scaffold-ma2:203753759            230.9             608026000        2633848.2
18:14:12.851 INFO  ProgressMeter - scaffold-ma2:204339176            231.0             608672000        2634742.8
18:14:22.868 INFO  ProgressMeter - scaffold-ma2:204931369            231.2             609324000        2635660.4
18:14:32.870 INFO  ProgressMeter - scaffold-ma2:205518166            231.4             609977000        2636583.8
18:14:37.032 INFO  CombineGVCFs - Shutting down engine
[July 18, 2022 6:14:37 PM CDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 245.07 minutes.
Runtime.totalMemory()=5240258560
org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at scaffold-ma2:205739202 [VC /scratch/07718/tg870175/Kat_combine_vcf/_vcf/CS0237.raw.snps.indels.g.vcf.gz @ scaffold-ma2:205739202 Q. of type=SYMBOLIC alleles=[T*, <NON_REF>] attr={END=205739202} GT=GT:DP:GQ:MIN_DP:PL 0/0:13:0:13:0,0,308 filters=
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:165)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    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)
Caused by: java.lang.NumberFormatException: For input string: "2?"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:580)
    at java.lang.Integer.parseInt(Integer.java:615)
    at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsInt(CommonInfo.java:316)
    at htsjdk.variant.variantcontext.VariantContext.getAttributeAsInt(VariantContext.java:819)
    at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.calculateVCDepth(ReferenceConfidenceVariantContextMerger.java:315)
    at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:135)
    at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:415)
    at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:229)
    at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:174)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:133)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:108)
    at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
    ... 21 more

Answer 1

[colindaven]

It doesn't like the string 2?, which is not a number. GATK expects a number, and Java is trying and failing to convert this into a number.

Caused by: java.lang.NumberFormatException: For input string: "2?"

Check your scaffolds for this string 2? and remove the ?