GenotypeGVCFs - A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader

[StefanoPallotti]

Dear all,

I'm trying to run GenotypeGVCFs using the my_folder database created with GenomicsDBImport which should contain 222 samples.

The database was created by adding progressively 10 samples at a time using the command --genomicsdb-update-workspace-path and the relative .sample_map file containing the path to my g.vcf.gz and g.vcf.gz.tbi files.

I tried running the GenomicsDBImport followed by GenotypeGVCFs using only four sampled and it worked appropriately by generating a .vcf.gz file along with the index .vcf.gz.tbi file.

However, when I run GenotypeGVCFs with 222 samples I get the error: A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader

The GATK version used is gatk-4.4.0.0 and the command used is the following:

python2.7 /home/administrator/tool/gatk-4.4.0.0/gatk --java-options "-Xmx4g" GenotypeGVCFs -R /mnt/nas/Stefano/Cashmere/Reference_Genome/GCF_001704415.1_ARS1_genomic.fna -V gendb://my_database -O /mnt/nas2/Stefano/Cashmere/joint_variant_calling/222_goats.vcf.gz

attaches below also the complete program log. and the content of my callset.json file.

Any idea about that?

Thank you very much.

Stefano

REQUIRED for all errors and issues:
a) GATK version used: gatk-4.4.0.0
b) Exact command used: python2.7 /home/administrator/tool/gatk-4.4.0.0/gatk --java-options "-Xmx4g" GenotypeGVCFs -R /mnt/nas/Stefano/Cashmere/Reference_Genome/GCF_001704415.1_ARS1_genomic.fna -V gendb://my_database -O /mnt/nas2/Stefano/Cashmere/joint_variant_calling/222_goats_fatte_con_GenomicsDBImport.vcf.gz

c) Entire program log:

(base) administrator@srv2-napolioni:/mnt/nas2/Stefano/Cashmere/joint_variant_calling$ python2.7 /home/administrator/tool/gatk-4.4.0.0/gatk --java-options "-Xmx4g" GenotypeGVCFs -R /mnt/nas/Stefano/Cashmere/Reference_Genome/GCF_001704415.1_ARS1_genomic.fna -V gendb://my_database -O /mnt/nas2/Stefano/Cashmere/joint_variant_calling/222_goats.vcf.gz
Using GATK jar /home/administrator/tool/gatk-4.4.0.0/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 -Xmx4g -jar /home/administrator/tool/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar GenotypeGVCFs -R /mnt/nas/Stefano/Cashmere/Reference_Genome/GCF_001704415.1_ARS1_genomic.fna -V gendb://my_database -O /mnt/nas2/Stefano/Cashmere/joint_variant_calling/222_goats.vcf.gz
12:01:18.521 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/administrator/tool/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:01:18.564 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:01:18.567 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.4.0.0
12:01:18.567 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
12:01:18.568 INFO  GenotypeGVCFs - Executing as administrator@srv2-napolioni on Linux v5.15.0-73-generic amd64
12:01:18.568 INFO  GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v19.0.2+7-Ubuntu-0ubuntu322.04
12:01:18.568 INFO  GenotypeGVCFs - Start Date/Time: March 1, 2024 at 12:01:18 PM UTC
12:01:18.568 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:01:18.568 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:01:18.569 INFO  GenotypeGVCFs - HTSJDK Version: 3.0.5
12:01:18.569 INFO  GenotypeGVCFs - Picard Version: 3.0.0
12:01:18.569 INFO  GenotypeGVCFs - Built for Spark Version: 3.3.1
12:01:18.570 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:01:18.570 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:01:18.570 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:01:18.570 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:01:18.570 INFO  GenotypeGVCFs - Deflater: IntelDeflater
12:01:18.571 INFO  GenotypeGVCFs - Inflater: IntelInflater
12:01:18.571 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
12:01:18.571 INFO  GenotypeGVCFs - Requester pays: disabled
12:01:18.571 INFO  GenotypeGVCFs - Initializing engine
12:01:19.353 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.4.4-ce4e1b9
12:01:33.262 INFO  NativeGenomicsDB - pid=1923139 tid=1923140 No valid combination operation found for INFO field InbreedingCoeff  - the field will NOT be part of INFO fields in the generated VCF records
12:01:33.262 INFO  NativeGenomicsDB - pid=1923139 tid=1923140 No valid combination operation found for INFO field MLEAC  - the field will NOT be part of INFO fields in the generated VCF records
12:01:33.262 INFO  NativeGenomicsDB - pid=1923139 tid=1923140 No valid combination operation found for INFO field MLEAF  - the field will NOT be part of INFO fields in the generated VCF records
12:01:33.288 INFO  GenotypeGVCFs - Shutting down engine
[March 1, 2024 at 12:01:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.25 minutes.
Runtime.totalMemory()=1130364928

---

A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader

---

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

 
content of my callset.json file:

{"callsets": [{"sample_name": "ERR318225","row_idx": 223,"idx_in_file": 0,"stream_name": "ERR318225_stream"},{"sample_name": "ERR318226","row_idx": 224,"idx_in_file": 0,"stream_name": "ERR318226_stream"},{"sample_name": "ERR4133262","row_idx": 225,"idx_in_file": 0,"stream_name": "ERR4133262_stream"},{"sample_name": "ERR4133361","row_idx": 226,"idx_in_file": 0,"stream_name": "ERR4133361_stream"},{"sample_name": "ERR4133400","row_idx": 227,"idx_in_file": 0,"stream_name": "ERR4133400_stream"},{"sample_name": "ERR4133407","row_idx": 228,"idx_in_file": 0,"stream_name": "ERR4133407_stream"},{"sample_name": "ERR4133418","row_idx": 229,"idx_in_file": 0,"stream_name": "ERR4133418_stream"},{"sample_name": "ERR4133445","row_idx": 230,"idx_in_file": 0,"stream_name": "ERR4133445_stream"},{"sample_name": "ERR4133451","row_idx": 231,"idx_in_file": 0,"stream_name": "ERR4133451_stream"},{"sample_name": "ERR4133452","row_idx": 232,"idx_in_file": 0,"stream_name": "ERR4133452_stream"},{"sample_name": "ERR4133453","row_idx": 233,"idx_in_file": 0,"stream_name": "ERR4133453_stream"},{"sample_name": "ERR4133456","row_idx": 234,"idx_in_file": 0,"stream_name": "ERR4133456_stream"},{"sample_name": "ERR4133303","row_idx": 200,"idx_in_file": 0,"stream_name": "ERR4133303_stream"},{"sample_name": "ERR4133306","row_idx": 201,"idx_in_file": 0,"stream_name": "ERR4133306_stream"},{"sample_name": "ERR4133327","row_idx": 202,"idx_in_file": 0,"stream_name": "ERR4133327_stream"},{"sample_name": "ERR4133337","row_idx": 203,"idx_in_file": 0,"stream_name": "ERR4133337_stream"},{"sample_name": "ERR4133351","row_idx": 204,"idx_in_file": 0,"stream_name": "ERR4133351_stream"},{"sample_name": "ERR4133353","row_idx": 205,"idx_in_file": 0,"stream_name": "ERR4133353_stream"},{"sample_name": "ERR4133355","row_idx": 206,"idx_in_file": 0,"stream_name": "ERR4133355_stream"},{"sample_name": "ERR4133359","row_idx": 207,"idx_in_file": 0,"stream_name": "ERR4133359_stream"},{"sample_name": "ERR4133360","row_idx": 208,"idx_in_file": 0,"stream_name": "ERR4133360_stream"},{"sample_name": "ERR4133442","row_idx": 209,"idx_in_file": 0,"stream_name": "ERR4133442_stream"},{"sample_name": "ERR4133302","row_idx": 190,"idx_in_file": 0,"stream_name": "ERR4133302_stream"},{"sample_name": "ERR4133312","row_idx": 191,"idx_in_file": 0,"stream_name": "ERR4133312_stream"},{"sample_name": "ERR4133335","row_idx": 192,"idx_in_file": 0,"stream_name": "ERR4133335_stream"},{"sample_name": "ERR4133340","row_idx": 193,"idx_in_file": 0,"stream_name": "ERR4133340_stream"},{"sample_name": "ERR4133541","row_idx": 194,"idx_in_file": 0,"stream_name": "ERR4133541_stream"},{"sample_name": "ERR4133544","row_idx": 195,"idx_in_file": 0,"stream_name": "ERR4133544_stream"},{"sample_name": "ERR4133545","row_idx": 196,"idx_in_file": 0,"stream_name": "ERR4133545_stream"},{"sample_name": "ERR4133553","row_idx": 197,"idx_in_file": 0,"stream_name": "ERR4133553_stream"},{"sample_name": "ERR4133555","row_idx": 198,"idx_in_file": 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[nalinigans]

Is it possible to run gatk with --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print a stack trace. Something along the lines of

gatk --java-options "-Xmx4g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" GenotypeGVCFs -R /mnt/nas/Stefano/Cashmere/Reference_Genome/GCF_001704415.1_ARS1_genomic.fna -V gendb://my_database -O /mnt/nas2/Stefano/Cashmere/joint_variant_calling/222_goats.vcf.gz