Dear,

I am trying to genotype SNPs from a set of > 1000 WGS samples. Following the "Biggest Practices" the g.vcf files have been reblocked, and after GenomicsDBimport, I was trying to obtain the final vcf file, using GnarlyGenotyper.

Running on a small interval for testing pourposes, it took 146 minutes, but the output is empty.

In the log there is the following warning:

12:29:57.666 WARN  GnarlyGenotyper - At least one variant cannot be genotyped because it is missing the QUALapproxkey assigned by the ReblockGVCFs tool. GnarlyGenotyper output may be empty.

Is there a solution to obtain the genotipic data out of the DB?

Thanks for any advice.

REQUIRED for all errors and issues:
a) GATK version used: gatk-4.6.0.0

b) Exact command used:

gatk --java-options "-Xmx80g -Xms80g" GnarlyGenotyper \
-R /u/xxx/reference/xxx.fasta \
-V gendb://xxx/gatk_db_import/chr01 \
-O /u/xxx/chr01.vcf.gz \
-L xxx/test.interval_list \
--tmp-dir /u/xxx/tmp/ \
--heterozygosity 0.01 \
--max-alternate-alleles 4 \
--merge-input-intervals

c) Entire program log:

Using GATK jar /xxx/gatk-4.6.0.0/gatk-package-4.6.0.0-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 -Xmx80g -Xms80g -jar /xxx/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar GnarlyGenotyper -R /u/xxx/reference/xxx.fasta -V gendb://xxx/chr01 -O /u/xxx/chr01.vcf.gz -L xxx/test.interval_list --tmp-dir /u/xxx/tmp/ --heterozygosity 0.01 --max-alternate-alleles 4 --merge-input-intervals
10:03:12.424 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/xxx/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl
10:03:12.424 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/xxx/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl
_compression.so                                                                                                                                                                                                                                               10:03:12.547 INFO  GnarlyGenotyper - ------------------------------------------------------------
10:03:12.550 INFO  GnarlyGenotyper - The Genome Analysis Toolkit (GATK) v4.6.0.0
10:03:12.550 INFO  GnarlyGenotyper - For support and documentation go to https://software.broadinstitute.org/gatk/
10:03:12.550 INFO  GnarlyGenotyper - Executing as xxx@xxx.hpc on Linux v6.10.3-200.fc40.x86_64 amd64
10:03:12.551 INFO  GnarlyGenotyper - Java runtime: OpenJDK 64-Bit Server VM v22.0.1-internal-adhoc.conda.src
10:03:12.551 INFO  GnarlyGenotyper - Start Date/Time: December 11, 2024, 10:03:12 AM CET
10:03:12.551 INFO  GnarlyGenotyper - ------------------------------------------------------------
10:03:12.551 INFO  GnarlyGenotyper - ------------------------------------------------------------
10:03:12.552 INFO  GnarlyGenotyper - HTSJDK Version: 4.1.1
10:03:12.552 INFO  GnarlyGenotyper - Picard Version: 3.2.0
10:03:12.553 INFO  GnarlyGenotyper - Built for Spark Version: 3.5.0
10:03:12.553 INFO  GnarlyGenotyper - HTSJDK Defaults.COMPRESSION_LEVEL : 2                                                                                                                     10:03:12.553 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:03:12.554 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:03:12.554 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:03:12.555 INFO  GnarlyGenotyper - Deflater: IntelDeflater
10:03:12.555 INFO  GnarlyGenotyper - Inflater: IntelInflater
10:03:12.555 INFO  GnarlyGenotyper - GCS max retries/reopens: 20
10:03:12.555 INFO  GnarlyGenotyper - Requester pays: disabled
10:03:12.555 WARN  GnarlyGenotyper -

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: GnarlyGenotyper is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

10:03:12.555 INFO  GnarlyGenotyper - Initializing engine
10:03:12.830 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.5.3-b586a26
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AC  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AF  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AN  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_BaseQRankSum  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_FS  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_InbreedingCoeff  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_MQ  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_MQRankSum  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_QD  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_ReadPosRankSum  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field AS_SOR  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field FS  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field InbreedingCoeff  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field QD  - the field will NOT be part of INFO fields in the generated VCF records
10:03:17.321 INFO  NativeGenomicsDB - pid=1968181 tid=1968182 No valid combination operation found for INFO field SOR  - the field will NOT be part of INFO fields in the generated VCF records10:03:21.741 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///xxx/test.interval_list
10:03:21.755 INFO  IntervalArgumentCollection - Processing 5038 bp from intervals
10:03:21.768 INFO  GnarlyGenotyper - Done initializing engine
10:03:21.981 INFO  Reflections - Reflections took 137 ms to scan 1 urls, producing 11 keys and 39 values
10:03:22.075 INFO  Reflections - Reflections took 91 ms to scan 1 urls, producing 11 keys and 39 values
10:03:22.075 INFO  ProgressMeter - Starting traversal
10:03:22.076 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

12:29:57.666 WARN  GnarlyGenotyper - At least one variant cannot be genotyped because it is missing the QUALapproxkey assigned by the ReblockGVCFs tool. GnarlyGenotyper output may be empty.
12:29:59.456 INFO  ProgressMeter -        chr01:1762404            146.6                  1000              6.8
Chromosome chr01 position 1762808 (TileDB column 1762807) has too many alleles in the combined VCF record : 9 : current limit : 5. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),8.005722431999997,Cpu time(s),7.895096517999998
12:30:05.863 INFO  ProgressMeter -        chr01:1767066            146.7                  5038             34.3
12:30:05.863 INFO  ProgressMeter - Traversal complete. Processed 5038 total variants in 146.7 minutes.
12:30:05.869 INFO  GnarlyGenotyper - Shutting down engine
[December 11, 2024, 12:30:05 PM CET] org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper done. Elapsed time: 146.89 minutes.