REQUIRED for all errors and issues:
a) GATK version used: 

gatk4/4.4.0.0

b) Exact command used:

gatk CombineGVCFs \

     -R ${gencode_path}/hg38.fa \

     -V ${data_output}/15650_raw_variants.vcf \

     -V ${data_output}/61850_LYG-3_raw_variants.vcf \

     -V ${data_output}/752190_raw_variants.vcf \

     -V ${data_output}/814546_raw_variants.vcf \

     -O ${data_output}/cohort_g_raw_variants.vcf.gz

c) Entire program log:

--------------------------------------------------------------

Apply CombineGVCFs

--------------------------------------------------------------

Using GATK jar /risapps/rhel8/miniconda3/py39_4.12.0/envs/gatk4-4.4.0.0/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-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 -jar /risapps/rhel8/miniconda3/py39_4.12.0/envs/gatk4-4.4.0.0/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar CombineGVCFs -R /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/gencode/hg38/hg38.fa -V /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/15650_raw_variants.vcf -V /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/61850_LYG-3_raw_variants.vcf -V /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/752190_raw_variants.vcf -V /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/814546_raw_variants.vcf -O /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/cohort_g_raw_variants.vcf.gz

11:55:49.507 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/risapps/rhel8/miniconda3/py39_4.12.0/envs/gatk4-4.4.0.0/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

11:55:49.549 INFO  CombineGVCFs - ------------------------------------------------------------

11:55:49.552 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.4.0.0

11:55:49.552 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/

11:55:49.552 INFO  CombineGVCFs - Executing as fdarbaniyan@ldragon3 on Linux v4.18.0-425.3.1.el8.x86_64 amd64

11:55:49.552 INFO  CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v17.0.3-internal+0-adhoc..src

11:55:49.552 INFO  CombineGVCFs - Start Date/Time: June 25, 2024 at 11:55:49 AM CDT

11:55:49.553 INFO  CombineGVCFs - ------------------------------------------------------------

11:55:49.553 INFO  CombineGVCFs - ------------------------------------------------------------

11:55:49.553 INFO  CombineGVCFs - HTSJDK Version: 3.0.5

11:55:49.553 INFO  CombineGVCFs - Picard Version: 3.0.0

11:55:49.553 INFO  CombineGVCFs - Built for Spark Version: 3.3.1

11:55:49.554 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2

11:55:49.554 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

11:55:49.554 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

11:55:49.554 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

11:55:49.554 INFO  CombineGVCFs - Deflater: IntelDeflater

11:55:49.554 INFO  CombineGVCFs - Inflater: IntelInflater

11:55:49.554 INFO  CombineGVCFs - GCS max retries/reopens: 20

11:55:49.554 INFO  CombineGVCFs - Requester pays: disabled

11:55:49.555 INFO  CombineGVCFs - Initializing engine

11:55:49.937 INFO  FeatureManager - Using codec VCFCodec to read file file:///rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/15650_raw_variants.vcf

11:55:50.075 INFO  FeatureManager - Using codec VCFCodec to read file file:///rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/61850_LYG-3_raw_variants.vcf

11:55:50.349 INFO  FeatureManager - Using codec VCFCodec to read file file:///rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/752190_raw_variants.vcf

11:55:50.639 INFO  FeatureManager - Using codec VCFCodec to read file file:///rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/814546_raw_variants.vcf

11:55:51.388 INFO  CombineGVCFs - Done initializing engine

11:55:51.411 INFO  ProgressMeter - Starting traversal

11:55:51.412 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

11:55:51.544 INFO  CombineGVCFs - Shutting down engine

[June 25, 2024 at 11:55:51 AM CDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.03 minutes.

Runtime.totalMemory()=1224736768

org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at chr1:960463 [VC /rsrch6/scratch/hema_bio-Malignan/fdarbaniyan/Sattva_data/WES/P2007014_05162024/Bioinfirmagician_output/results/15650_raw_variants.vcf @ chr1:960463 Q73.64 of type=SNP alleles=[G*, T] attr={AC=1, AF=0.500, AN=2, BaseQRankSum=-0.967, DP=3, ExcessHet=0.0000, FS=0.000, MLEAC=1, MLEAF=0.500, MQ=60.00, MQRankSum=0.000, QD=24.55, ReadPosRankSum=-0.967, SOR=0.223} GT=GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 filters=

at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)

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:197)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)

at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)

at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)

at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)

at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)

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.forEach(ReferencePipeline.java:596)

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:1098)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)

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.IllegalStateException: Key END found in VariantContext field INFO at chr1:959226 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.

at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:215)

at htsjdk.variant.vcf.VCFEncoder.write(VCFEncoder.java:148)

at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:250)

at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:420)

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