Can you please provide
a) GATK version used: 4.1.7.0
Hello,

I have this problem with genotyping my GVCFs. As you can see from the error below, only 1 locus was genotyped and the vcf produced. I have checked my GVCFs and find them to be in order (with all the chromosome positions present).

gatk --java-options "-Xmx32g" GenotypeGVCFs \
> -R /home/himawari/REF/GRCh37/B37/human_g1k_v37.fasta \
> -V /home/himawari/SCD/OUTPUT/SCDO_3_X5/SCDO_3_X5.g.vcf.gz \
> -O /home/himawari/SCD/OUTPUT/SCDO_3_X5/SCDO_3_X5_test.vcf.gz
Using GATK jar /home/himawari/Downloads/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32g -jar /home/himawari/Downloads/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar GenotypeGVCFs -R /home/himawari/REF/GRCh37/B37/human_g1k_v37.fasta -V /home/himawari/SCD/OUTPUT/SCDO_3_X5/SCDO_3_X5.g.vcf.gz -O /home/himawari/SCD/OUTPUT/SCDO_3_X5/SCDO_3_X5_test.vcf.gz
18:53:00.022 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/himawari/Downloads/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 01, 2020 6:53:00 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
18:53:00.115 INFO GenotypeGVCFs - ------------------------------------------------------------
18:53:00.115 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.7.0
18:53:00.115 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
18:53:00.115 INFO GenotypeGVCFs - Executing as himawari@ncgm001 on Linux v4.15.0-101-generic amd64
18:53:00.115 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src
18:53:00.116 INFO GenotypeGVCFs - Start Date/Time: 1 June 2020 at 18:52:59 CST
18:53:00.116 INFO GenotypeGVCFs - ------------------------------------------------------------
18:53:00.116 INFO GenotypeGVCFs - ------------------------------------------------------------
18:53:00.116 INFO GenotypeGVCFs - HTSJDK Version: 2.21.2
18:53:00.116 INFO GenotypeGVCFs - Picard Version: 2.21.9
18:53:00.116 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:53:00.116 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:53:00.116 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:53:00.116 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:53:00.116 INFO GenotypeGVCFs - Deflater: IntelDeflater
18:53:00.116 INFO GenotypeGVCFs - Inflater: IntelInflater
18:53:00.116 INFO GenotypeGVCFs - GCS max retries/reopens: 20
18:53:00.116 INFO GenotypeGVCFs - Requester pays: disabled
18:53:00.116 INFO GenotypeGVCFs - Initializing engine
18:53:00.201 INFO FeatureManager - Using codec VCFCodec to read file file:///home/himawari/SCD/OUTPUT/SCDO_3_X5/SCDO_3_X5.g.vcf.gz
18:53:00.279 INFO GenotypeGVCFs - Done initializing engine
18:53:00.301 INFO ProgressMeter - Starting traversal
18:53:00.302 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:53:00.365 WARN InbreedingCoeff - InbreedingCoeff will not be calculated; at least 10 samples must have called genotypes
18:53:10.303 INFO ProgressMeter - 1:227192693 0.2 1197000 7181281.9
18:53:11.090 INFO GenotypeGVCFs - Shutting down engine
[1 June 2020 at 18:53:11 CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=1275068416
java.lang.IllegalArgumentException: Invalid interval. Contig:1 start:249213232 end:41385
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:733)
at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:59)
at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:35)
at org.broadinstitute.hellbender.utils.SimpleInterval.<init>(SimpleInterval.java:47)
at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:134)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:502)
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)

I am unsure where I am doing wrong.

BTW, I used CombineGVCFs to consolidate my GVCFs instead of GenomicsDB because I do not know how to use it properly. It took too long to consolidate. I am unsure of how to split it too. I think I don't quite understand it as well.

Himawari.