a) GATK version used: 4.2.5.0
b) Exact command used: ~/gatk-4.2.5.0/gatk --java-options "-Xms60G -Xmx240G" GenotypeGVCFs \
    -R ../ref/refseq2.1_assembly.fasta \
    -V gendb://GenomicsDB \
    --tmp-dir  ../tmpGATK  \
    -O out.vcf
c) Entire program log:

15:30:35.021 INFO  ProgressMeter - ChrUnknown:351578707           8856.5            9452663660        1067308.7

15:30:35.021 INFO  ProgressMeter - Traversal complete. Processed 9452663660 total variants in 8856.5 minutes.

15:30:36.176 INFO  GenotypeGVCFs - Shutting down engine
[November 30, 2022 3:30:36 PM EST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 8,856.65 minutes.
Runtime.totalMemory()=73348939776
Using GATK jar /home/AAFC-AAC/vasudevanak/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -Xms60G -Xmx240G -jar /home/AAFC-AAC/vasudevanak/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenotypeGVCFs -R ../ref/refseq2.1_assembly.fasta -V gendb://GenomicsDB --tmp-dir ../tmpGATK -O out.vcf

/opt/gridengine/default/spool/biocomp-0-7/job_scripts/15311: line 11: 54311 Bus error               (core dumped) ~/gatk-4.2.5.0/gatk --java-options "-Xms60G -Xmx240G" GenotypeGVCFs -R ../ref/refseq2.1_assembly.fasta  -V gendb://GenomicsDB --tmp-dir ../tmpGATK -O out.vcf

I ran GenotypeGVCFs using eight accessions, and the size of the genome for the species ~16Gb. With the available computation resources the program ran for about six days and the traversal was complete. However, I received a core dumped error at the end.

When I validated the output (huge) vcf file using GATK's ValidateVariants, I did not receive any red flags. 

Can you please advise if I can continue downstream analysis with the output VCF file or should the GenotypeGVCF file be rerun because of the error at the end after traversal.