I am encountering an issue when querying a GenomicsDB workspace generated by GenomicsDBImport.

I rebuilt the workspace from scratch and GenomicsDBImport completed successfully, but downstream tools such as SelectVariants and GenotypeGVCFs appear to hang when reading from the gendb:// workspace.

Here are the details of my setup:

GATK version: 4.6.2.0 Java: OpenJDK 21.0.6 OS: Linux x86_64 GenomicsDB native library version: 1.5.5-addd795

GenomicsDBImport command I used a per-chromosome import with 1250 samples:

gatk --java-options "-Xmx200g -Xms200g -Djava.io.tmpdir=/mnt/k/disease/temp" GenomicsDBImport
--genomicsdb-workspace-path /mnt/k/disease/GenomicsDB/chr1
--intervals chr1
--batch-size 60
--sample-name-map /mnt/k/disease/GenomicsDB/chr1.map
--reader-threads 10
--tmp-dir /mnt/k/disease/temp

The import completed successfully with the following ending in the log:

Done importing batch 21/21
Import of all batches to GenomicsDB completed!
Shutting down engine
Tool returned:
true
2. Workspace characteristics
Chromosome: chr1
Interval size processed during import: 35,787,290 bp
Number of samples: 1250

The workspace contains expected files such as:

callset.json
vidmap.json
vcfheader.vcf

1. Problematic downstream query

When I try to read the workspace using SelectVariants:

gatk --java-options "-Xmx8g -Djava.io.tmpdir=/mnt/k/tmp" SelectVariants
-R /mnt/k/disease/ref/genome.fa
-V gendb:///mnt/k/disease/GenomicsDB/chr1
-O /mnt/k/disease/vcf/chr1.vcf.gz

the tool starts normally, but then stops after:

Initializing engine
GenomicsDB native library version : 1.5.5-addd795
No valid combination operation found for INFO field InbreedingCoeff
No valid combination operation found for INFO field MLEAC
No valid combination operation found for INFO field MLEAF

and does not make further progress.