REQUIRED for all errors and issues:
a) GATK version used: 4.5.0.0
b) Exact command used: 

GATK_HEAP_SIZE=200g

REFERENCE="/scratch/genomics/holmk/bongo_genome/reference/HiCref_annot/barney_pseudo2.1_HiC.fasta"

rungatk CombineGVCFs -R $REFERENCE -O bongo_seqcap_raw.vcf \

--variant gvcfs.list

I am trying to combine my gvcf files from HaplotypeCaller. I tried using GenomicsDBImport but it ran out of memory 10 days into it. This variant calling is for target capture and I used my target bed file as the -L intervals. This may not have been correct.

mkdir -p temp/$JOB_ID

GATK_HEAP_SIZE=200g

Commands:

gatk GenomicsDBImport \

    --genomicsdb-workspace-path genomicsworkspace \

    --batch-size 50 \

    --sample-name-map sample_map.txt \

    --max-num-intervals-to-import-in-parallel 3 \

    --tmp-dir temp/$JOB_ID \

    --intervals ../../bwa-mem/SNPs_target_mod.bed

So I tried using CombineGVCF instead due to the memory issue and I got this error in the log file after 3 days.

22:55:35.867 INFO  CombineGVCFs - Done initializing engine

22:55:36.181 INFO  ProgressMeter - Starting traversal

22:55:36.182 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

22:55:38.265 WARN  CombineGVCFs - Error: The requested interval contained no data in source VCF files

22:55:38.266 INFO  ProgressMeter -             unmapped              0.0                     0              0.0

22:55:38.266 INFO  ProgressMeter - Traversal complete. Processed 0 total variants in 0.0 minutes.

22:55:38.266 WARN  CombineGVCFs - Error: The requested interval contained no data in source VCF files

22:55:38.302 INFO  CombineGVCFs - Shutting down engine

[September 16, 2024 at 10:55:38 PM EDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 4,897.95 minutes.

Runtime.totalMemory()=23175397376

= Mon Sep 16 22:55:38 EDT 2024 job bongo_combinegVCF done

I did not use an interval list for this.  I am not actually sure what the interval list should be. I have over 35000 contigs, some are chromosome length. It did produce a vcf file, just not sure it is correct.

Thanks for any insight! Karen