I have been running the GATK4 pipeline for whole genome sequencing of a non-model organism (salmon). I successfully imported all of my g.vcf files into a database with GenomicsDBImport and am now genotyping them using genotypeGVCFs. 

27 of the 29 scaffolds worked smoothly, but two scaffolds cause genotypeGVCFs to stop. In both cases, I recreated a database for each scaffold, but re-running genotypeGVCFs still quit at the same point for both scaffolds. 

Given that genotypeGVCFs stops at a consistent location, my guess was that it is an error in how the g.vcfs or alignment files were built. But am not sure why this would effect only a some scaffolds. Also, I would like to avoid having to realign everything to fix the issue. I have pasted the tail end of the output below that includes the java error starting with "java.lang.NullPointerException"

23:28:07.332 INFO  ProgressMeter -  NC_042563.1:8112541            147.5               7938000          53816.3

23:28:38.725 INFO  ProgressMeter -  NC_042563.1:8118541            148.0               7944000          53666.6

23:28:44.041 INFO  GenotypeGVCFs - Shutting down engine

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6726.439935984614,Cpu time(s),3195.8068186542678

[August 28, 2020 11:28:44 PM GMT-05:00] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 148.28 minutes.

Runtime.totalMemory()=73499934720

java.lang.NullPointerException

at htsjdk.variant.bcf2.BCF2Decoder.decodeInt(BCF2Decoder.java:226)

at htsjdk.variant.bcf2.BCF2Decoder.decodeSingleValue(BCF2Decoder.java:157)

at htsjdk.variant.bcf2.BCF2Decoder.decodeTypedValue(BCF2Decoder.java:146)

at htsjdk.variant.bcf2.BCF2Decoder.decodeTypedValue(BCF2Decoder.java:130)

at htsjdk.variant.bcf2.BCF2Decoder.decodeTypedValue(BCF2Decoder.java:125)

at htsjdk.variant.bcf2.BCF2Codec.decodeInfo(BCF2Codec.java:410)

at htsjdk.variant.bcf2.BCF2Codec.decodeSitesExtendedInfo(BCF2Codec.java:298)

at htsjdk.variant.bcf2.BCF2Codec.decode(BCF2Codec.java:132)

at htsjdk.variant.bcf2.BCF2Codec.decode(BCF2Codec.java:58)

at org.genomicsdb.reader.GenomicsDBFeatureIterator.next(GenomicsDBFeatureIterator.java:183)

at org.genomicsdb.reader.GenomicsDBFeatureIterator.next(GenomicsDBFeatureIterator.java:49)

at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.loadNextFeature(FeatureIntervalIterator.java:98)

at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.loadNextNovelFeature(FeatureIntervalIterator.java:74)

at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.next(FeatureIntervalIterator.java:62)

at org.broadinstitute.hellbender.engine.FeatureIntervalIterator.next(FeatureIntervalIterator.java:24)

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.forEachOrdered(ReferencePipeline.java:490)

at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)

at org.broadinstitute.hellbender.Main.main(Main.java:292)