Hi GATK team,

I'm in the process of using the biggest practices to generate a joint genotyped SNV/indel callset on ~55k human germline whole-genomes.

I've been able to successfully run the Gnarly genotyping pipeline on several chromosomes, but am encountering a persistent error with a specific position on chr21 that seems to be related to a Java string-to-integer formatting error in GnarlyGenotyper.

I've tried debugging this by checking the genomicsdb.tar input file, but didn't spot anything that was obviously incorrect.

I'd be really grateful if you might be able to provide some pointers on debugging this issue!

Here are the technical details:

• GATK version: 4.6.1.0, executed via Cromwell using Docker (`us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-10-25-v0.29-beta-5ea22a52`)

• Exact command used: 

gatk --java-options "-Xms8000m -Xmx25000m" \
  GnarlyGenotyper \
  -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta \
  -O dfci-g2c.v1.chr21.patch.5.0.vcf.gz \
  -D gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf \
  --only-output-calls-starting-in-intervals \
  -V gendb://$WORKSPACE \
  -L gs://fc-secure-29075a92-7950-4778-aa20-874a75cd37bf/cromwell/execution/GnarlyJointGenotypingPart1/6f5bf4f3-cf87-40ff-bc8c-46ed85202654/call-G2CSplitIntervals/glob-5db530f76090fc6b87003e11af3127d1/000006-scattered.interval_list \
  -stand-call-conf 10 \
  --max-alternate-alleles 5 \
  --merge-input-intervals

• Entire program log:

Using GATK jar /gatk/gatk-package-4.6.1.0-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 -Xms8000m -Xmx25000m -jar /gatk/gatk-package-4.6.1.0-local.jar GnarlyGenotyper -R/cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -O dfci-g2c.v1.chr21.patch.5.0.vcf.gz -D gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf --only-output-calls-starting-in-intervals -V gendb://genomicsdb -L gs://fc-secure-29075a92-7950-4778-aa20-874a75cd37bf/cromwell/execution/GnarlyJointGenotypingPart1/6f5bf4f3-cf87-40ff-bc8c-46ed85202654/call-G2CSplitIntervals/glob-5db530f76090fc6b87003e11af3127d1/000006-scattered.interval_list -stand-call-conf 10 --max-alternate-alleles 5 --merge-input-intervals
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.06JHXL
23:55:20.054 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.6.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
SLF4J(W): Class path contains multiple SLF4J providers.
SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@27898e13]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@4f5f474c]
SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@27898e13]
23:55:20.100 INFO  GnarlyGenotyper - ------------------------------------------------------------
23:55:20.103 INFO  GnarlyGenotyper - The Genome Analysis Toolkit (GATK) v4.6.1.0
23:55:20.103 INFO  GnarlyGenotyper - For support and documentation go to https://software.broadinstitute.org/gatk/
23:55:20.103 INFO  GnarlyGenotyper - Executing as root@dff50889227e on Linux v6.6.72+ amd64
23:55:20.103 INFO  GnarlyGenotyper - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
23:55:20.104 INFO  GnarlyGenotyper - Start Date/Time: March 19, 2025 at 11:55:19 PM GMT
23:55:20.104 INFO  GnarlyGenotyper - ------------------------------------------------------------
23:55:20.104 INFO  GnarlyGenotyper - ------------------------------------------------------------
23:55:20.105 INFO  GnarlyGenotyper - HTSJDK Version: 4.1.3
23:55:20.105 INFO  GnarlyGenotyper - Picard Version: 3.3.0
23:55:20.106 INFO  GnarlyGenotyper - Built for Spark Version: 3.5.0
23:55:20.109 INFO  GnarlyGenotyper - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:55:20.109 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:55:20.110 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:55:20.110 INFO  GnarlyGenotyper - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:55:20.110 INFO  GnarlyGenotyper - Deflater: IntelDeflater
23:55:20.110 INFO  GnarlyGenotyper - Inflater: IntelInflater
23:55:20.111 INFO  GnarlyGenotyper - GCS max retries/reopens: 20
23:55:20.111 INFO  GnarlyGenotyper - Requester pays: disabled
23:55:20.111 WARN  GnarlyGenotyper -

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

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

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


23:55:20.112 INFO  GnarlyGenotyper - Initializing engine
23:55:22.078 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
23:55:23.676 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.5.4-764a03c
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AC  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AF  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AN  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_BaseQRankSum- the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_FS  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_InbreedingCoeff  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_MQ  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_MQRankSum  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.260 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_QD  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_ReadPosRankSum  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field AS_SOR  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field FS  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field InbreedingCoeff- the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field QD  - the field will NOT be part of INFO fields in the generated VCF records
23:55:24.261 INFO  NativeGenomicsDB - pid=107 tid=108 No valid combination operation found for INFO field SOR  - the fieldwill NOT be part of INFO fields in the generated VCF records
23:55:26.663 INFO  FeatureManager - Using codec IntervalListCodec to read file gs://fc-secure-29075a92-7950-4778-aa20-874a75cd37bf/cromwell/execution/GnarlyJointGenotypingPart1/6f5bf4f3-cf87-40ff-bc8c-46ed85202654/call-G2CSplitIntervals/glob-5db530f76090fc6b87003e11af3127d1/000006-scattered.interval_list
23:55:27.055 INFO  IntervalArgumentCollection - Processing 20141 bp from intervals
23:55:27.112 INFO  GnarlyGenotyper - Done initializing engine
23:55:27.113 WARN  GnarlyGenotyper - The --only-output-calls-starting-in-intervals option is deprecated. Please use '--variant-output-filtering STARTS_IN' for an equivalent filtering.
23:55:27.511 INFO  Reflections - Reflections took 147 ms to scan 1 urls, producing 11 keys and 39 values
23:55:27.615 INFO  Reflections - Reflections took 101 ms to scan 1 urls, producing 11 keys and 39 values
23:55:27.616 INFO  ProgressMeter - Starting traversal
23:55:27.617 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
Chromosome chr21 position 8202866 (TileDB column 2785675936) has too many alleles in the combined VCF record : 14 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

23:57:34.449 INFO  ProgressMeter -        chr21:8203459              2.1                  1000            473.1
Chromosome chr21 position 8203682 (TileDB column 2785676752) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

23:58:09.494 INFO  ProgressMeter -        chr21:8204486              2.7                  2000            741.3
Chromosome chr21 position 8208018 (TileDB column 2785681088) has too many alleles in the combined VCF record : 13 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8208019 (TileDB column 2785681089) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

23:59:33.733 INFO  ProgressMeter -        chr21:8208113              4.1                  3000            731.4
Chromosome chr21 position 8208479 (TileDB column 2785681549) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8208493 (TileDB column 2785681563) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8209111 (TileDB column 2785682181) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8209116 (TileDB column 2785682186) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8209117 (TileDB column 2785682187) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:04:36.516 INFO  ProgressMeter -        chr21:8209113              9.1                  4000            437.2
Chromosome chr21 position 8209118 (TileDB column 2785682188) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:05:22.608 INFO  ProgressMeter -        chr21:8211351              9.9                  5000            504.2
Chromosome chr21 position 8211686 (TileDB column 2785684756) has too many alleles in the combined VCF record : 16 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8211705 (TileDB column 2785684775) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8211707 (TileDB column 2785684777) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8211709 (TileDB column 2785684779) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:06:02.619 INFO  ProgressMeter -        chr21:8212714             10.6                  6000            566.9
Chromosome chr21 position 8212916 (TileDB column 2785685986) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8212952 (TileDB column 2785686022) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213080 (TileDB column 2785686150) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213131 (TileDB column 2785686201) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213183 (TileDB column 2785686253) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213185 (TileDB column 2785686255) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213285 (TileDB column 2785686355) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213335 (TileDB column 2785686405) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213338 (TileDB column 2785686408) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213339 (TileDB column 2785686409) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213361 (TileDB column 2785686431) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213393 (TileDB column 2785686463) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213394 (TileDB column 2785686464) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213402 (TileDB column 2785686472) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213441 (TileDB column 2785686511) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8213602 (TileDB column 2785686672) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:12:19.455 INFO  ProgressMeter -        chr21:8213714             16.9                  7000            415.1
Chromosome chr21 position 8214405 (TileDB column 2785687475) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214454 (TileDB column 2785687524) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214473 (TileDB column 2785687543) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214495 (TileDB column 2785687565) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214497 (TileDB column 2785687567) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214501 (TileDB column 2785687571) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214505 (TileDB column 2785687575) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214520 (TileDB column 2785687590) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214628 (TileDB column 2785687698) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214648 (TileDB column 2785687718) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214649 (TileDB column 2785687719) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214650 (TileDB column 2785687720) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214658 (TileDB column 2785687728) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214669 (TileDB column 2785687739) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214671 (TileDB column 2785687741) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214672 (TileDB column 2785687742) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214676 (TileDB column 2785687746) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214679 (TileDB column 2785687749) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:18:16.466 INFO  ProgressMeter -        chr21:8214714             22.8                  8000            350.7
Chromosome chr21 position 8214732 (TileDB column 2785687802) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214734 (TileDB column 2785687804) has too many alleles in the combined VCF record : 17 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214749 (TileDB column 2785687819) has too many alleles in the combined VCF record : 15 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214755 (TileDB column 2785687825) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214760 (TileDB column 2785687830) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214761 (TileDB column 2785687831) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214764 (TileDB column 2785687834) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214777 (TileDB column 2785687847) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214780 (TileDB column 2785687850) has too many alleles in the combined VCF record : 11 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214781 (TileDB column 2785687851) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214783 (TileDB column 2785687853) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214788 (TileDB column 2785687858) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214863 (TileDB column 2785687933) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214881 (TileDB column 2785687951) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214894 (TileDB column 2785687964) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214904 (TileDB column 2785687974) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214913 (TileDB column 2785687983) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214920 (TileDB column 2785687990) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8214956 (TileDB column 2785688026) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8215018 (TileDB column 2785688088) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8215104 (TileDB column 2785688174) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:23:07.684 INFO  ProgressMeter -        chr21:8215714             27.7                  9000            325.3
00:23:49.097 INFO  ProgressMeter -        chr21:8216714             28.4                 10000            352.6
Chromosome chr21 position 8216861 (TileDB column 2785689931) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8216926 (TileDB column 2785689996) has too many alleles in the combined VCF record : 10 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8216997 (TileDB column 2785690067) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217012 (TileDB column 2785690082) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217206 (TileDB column 2785690276) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217212 (TileDB column 2785690282) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217213 (TileDB column 2785690283) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217305 (TileDB column 2785690375) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217317 (TileDB column 2785690387) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217378 (TileDB column 2785690448) has too many alleles in the combined VCF record : 11 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217381 (TileDB column 2785690451) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217403 (TileDB column 2785690473) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8217405 (TileDB column 2785690475) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:28:41.920 INFO  ProgressMeter -        chr21:8217715             33.2                 11000            330.9
Chromosome chr21 position 8218901 (TileDB column 2785691971) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8218941 (TileDB column 2785692011) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8218946 (TileDB column 2785692016) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219053 (TileDB column 2785692123) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219067 (TileDB column 2785692137) has too many alleles in the combined VCF record : 13 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219074 (TileDB column 2785692144) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219246 (TileDB column 2785692316) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219347 (TileDB column 2785692417) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219351 (TileDB column 2785692421) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219354 (TileDB column 2785692424) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219502 (TileDB column 2785692572) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:32:27.479 INFO  ProgressMeter -        chr21:8219499             37.0                 12000            324.3
Chromosome chr21 position 8219891 (TileDB column 2785692961) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219892 (TileDB column 2785692962) has too many alleles in the combined VCF record : 19 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219897 (TileDB column 2785692967) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219899 (TileDB column 2785692969) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219900 (TileDB column 2785692970) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219901 (TileDB column 2785692971) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219902 (TileDB column 2785692972) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219903 (TileDB column 2785692973) has too many alleles in the combined VCF record : 29 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219905 (TileDB column 2785692975) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219908 (TileDB column 2785692978) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219909 (TileDB column 2785692979) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219911 (TileDB column 2785692981) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219915 (TileDB column 2785692985) has too many alleles in the combined VCF record : 13 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219917 (TileDB column 2785692987) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219919 (TileDB column 2785692989) has too many alleles in the combined VCF record : 13 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219921 (TileDB column 2785692991) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219923 (TileDB column 2785692993) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219925 (TileDB column 2785692995) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219927 (TileDB column 2785692997) has too many alleles in the combined VCF record : 13 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219929 (TileDB column 2785692999) has too many alleles in the combined VCF record : 43 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219931 (TileDB column 2785693001) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219933 (TileDB column 2785693003) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219935 (TileDB column 2785693005) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219937 (TileDB column 2785693007) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219941 (TileDB column 2785693011) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219947 (TileDB column 2785693017) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219951 (TileDB column 2785693021) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219953 (TileDB column 2785693023) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219956 (TileDB column 2785693026) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219962 (TileDB column 2785693032) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219966 (TileDB column 2785693036) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219969 (TileDB column 2785693039) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219970 (TileDB column 2785693040) has too many alleles in the combined VCF record : 7 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219985 (TileDB column 2785693055) has too many alleles in the combined VCF record : 14 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8219998 (TileDB column 2785693068) has too many alleles in the combined VCF record : 14 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220002 (TileDB column 2785693072) has too many alleles in the combined VCF record : 11 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220006 (TileDB column 2785693076) has too many alleles in the combined VCF record : 11 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220012 (TileDB column 2785693082) has too many alleles in the combined VCF record : 17 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220024 (TileDB column 2785693094) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220027 (TileDB column 2785693097) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220028 (TileDB column 2785693098) has too many alleles in the combined VCF record : 9 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220029 (TileDB column 2785693099) has too many alleles in the combined VCF record : 12 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220031 (TileDB column 2785693101) has too many alleles in the combined VCF record : 40 : current limit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

Chromosome chr21 position 8220033 (TileDB column 2785693103) has too many alleles in the combined VCF record : 8 : currentlimit : 6. Fields, such as  PL, with length equal to the number of genotypes will NOT be added for this location.

00:37:27.737 INFO  GnarlyGenotyper - Shutting down engine
GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),1780.0524901770002,Cpu time(s),1773.6591073770003
[March 20, 2025 at 12:37:28 AM GMT] org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper done. Elapsed time: 42.14 minutes.
Runtime.totalMemory()=8388608000
java.lang.NumberFormatException: For input string: "2707900110"
        at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
        at java.base/java.lang.Integer.parseInt(Integer.java:668)
        at java.base/java.lang.Integer.parseInt(Integer.java:786)
        at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsInt(CommonInfo.java:316)
        at htsjdk.variant.variantcontext.VariantContext.getAttributeAsInt(VariantContext.java:842)
        at org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine.finalizeGenotype(GnarlyGenotyperEngine.java:86)
        at org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine.finalizeGenotype(GnarlyGenotyperEngine.java:69)
        at org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper.apply(GnarlyGenotyper.java:288)
        at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
        at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
        at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
        at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)

Thanks in advance for any help you can provide!