gatk GenotypeGVCFs --force-output-intervals bug

GenotypeGVCFs --force-output-intervals bug

Open GATKSupportTeam opened this issue 2 years ago • 1 comments

Discussed in office hours. Seems to be a bug with --force-output-intervals in GenotypeGVCFs when using GenomicsDB.

This request was created from a contribution made by Zane Swaydan on June 30, 2022 11:13 UTC.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/6972994559643-java-lang-IllegalStateException-in-GenotypeGVCFs-after-GenomicsDBImport-GATK-4-2-6-1

I'm using the GenotypeGVCFs function based on GenomicsDBImport database. I've divided the reference into 50 intervals. Some intervals seems ok, but some reports error as following.

I used a VCF file in "--force-output-intervals" for down stream analysis. I've never seen this error without "--force-output-intervals". I've searched for the error message and changed my GATK version to 4.2.6.1 since similar error has been solved as a bug in recent update, but it still not works on my dataset...

REQUIRED for all errors and issues:

a) GATK version used:

GenomicsDBImport: GATK 4.2.4.0

GenotypeGVCFs: GATK 4.2.6.1

b) Exact command used:

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 -Xms4G -Xmx16G -XX:+UseParallelGC -XX:ParallelGCThreads=2 -jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenotypeGVCFs -R PigeonBatch5/000_DataLinks/000_RefSeq/Cliv2.1_genomic.fasta --intervals 006_IntervalsSplit_DBImport_VCFref/interval_9.list --force-output-intervals PigeonBatch4/008_RawVcfGz/MergeVcf/pigeonBatch1234_filtered.vcf.gz -V gendb://007_Database_DBImport_VCFref/database_interval_9 -O 008_RawVcfGz_DBImport_VCFref/001_DividedIntervals/interval_9.vcf.gz --tmp-dir TMPDIR --allow-old-rms-mapping-quality-annotation-data --only-output-calls-starting-in-intervals --verbosity ERROR

c) Entire program log:

Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

Running:

15:30:47.303 info NativeGenomicsDB - pid=135716 tid=135717 No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records

15:30:47.303 info NativeGenomicsDB - pid=135716 tid=135717 No valid combination operation found for INFO field HaplotypeScore - the field will NOT be part of INFO fields in the generated VCF records

15:30:47.303 info NativeGenomicsDB - pid=135716 tid=135717 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records

15:30:47.303 info NativeGenomicsDB - pid=135716 tid=135717 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records

15:30:47.303 info NativeGenomicsDB - pid=135716 tid=135717 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),91.7218584799977,Cpu time(s),62.47174291199972

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.00229105499993,Cpu time(s),62.04487875900044

Sample/Callset COLI0776( TileDB row idx 0) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI0807( TileDB row idx 1) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI0855( TileDB row idx 2) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI0874( TileDB row idx 3) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI0998( TileDB row idx 4) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1023( TileDB row idx 5) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1032( TileDB row idx 6) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1040( TileDB row idx 7) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1059( TileDB row idx 8) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1179( TileDB row idx 9) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1222( TileDB row idx 10) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1270( TileDB row idx 11) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1272( TileDB row idx 12) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1307( TileDB row idx 13) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1396( TileDB row idx 14) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1433( TileDB row idx 15) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1510( TileDB row idx 16) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1555( TileDB row idx 17) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1585( TileDB row idx 18) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1596( TileDB row idx 19) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1652( TileDB row idx 20) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1686( TileDB row idx 21) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1785( TileDB row idx 22) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1861( TileDB row idx 23) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI1959( TileDB row idx 24) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2026( TileDB row idx 25) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2045( TileDB row idx 26) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2100( TileDB row idx 27) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2116( TileDB row idx 28) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2158( TileDB row idx 29) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2199( TileDB row idx 30) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2239( TileDB row idx 31) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2350( TileDB row idx 32) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2354( TileDB row idx 33) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2414( TileDB row idx 34) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2422( TileDB row idx 35) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2462( TileDB row idx 36) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2488( TileDB row idx 37) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2548( TileDB row idx 38) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2556( TileDB row idx 39) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2678( TileDB row idx 40) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2714( TileDB row idx 41) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2773( TileDB row idx 42) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2775( TileDB row idx 43) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2800( TileDB row idx 44) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2816( TileDB row idx 45) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2819( TileDB row idx 46) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2843( TileDB row idx 47) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2957( TileDB row idx 48) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2968( TileDB row idx 49) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI2980( TileDB row idx 50) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3132( TileDB row idx 51) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3152( TileDB row idx 52) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3205( TileDB row idx 53) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3235( TileDB row idx 54) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3277( TileDB row idx 55) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3380( TileDB row idx 56) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3385( TileDB row idx 57) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3407( TileDB row idx 58) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3428( TileDB row idx 59) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3585( TileDB row idx 60) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3669( TileDB row idx 61) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3713( TileDB row idx 62) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3722( TileDB row idx 63) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3723( TileDB row idx 64) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3740( TileDB row idx 65) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLI3787( TileDB row idx 66) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0154( TileDB row idx 67) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0160( TileDB row idx 68) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0199( TileDB row idx 69) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0229( TileDB row idx 70) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0238( TileDB row idx 71) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0391( TileDB row idx 72) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0514( TileDB row idx 73) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0537( TileDB row idx 74) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0551( TileDB row idx 75) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0634( TileDB row idx 76) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0728( TileDB row idx 78) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0787( TileDB row idx 80) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0903( TileDB row idx 81) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV0920( TileDB row idx 82) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1022( TileDB row idx 83) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1075( TileDB row idx 84) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1090( TileDB row idx 85) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1115( TileDB row idx 86) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1212( TileDB row idx 87) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1235( TileDB row idx 88) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1237( TileDB row idx 89) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1310( TileDB row idx 90) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1355( TileDB row idx 91) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1463( TileDB row idx 92) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1526( TileDB row idx 94) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1536( TileDB row idx 95) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1550( TileDB row idx 96) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1563( TileDB row idx 97) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1606( TileDB row idx 98) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1614( TileDB row idx 99) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1616( TileDB row idx 100) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1617( TileDB row idx 101) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1647( TileDB row idx 102) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1648( TileDB row idx 103) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1706( TileDB row idx 104) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1791( TileDB row idx 105) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1814( TileDB row idx 106) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1815( TileDB row idx 107) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1855( TileDB row idx 108) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1872( TileDB row idx 109) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1884( TileDB row idx 110) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1931( TileDB row idx 111) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV1964( TileDB row idx 112) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2003( TileDB row idx 113) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2074( TileDB row idx 114) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2131( TileDB row idx 115) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2132( TileDB row idx 116) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2140( TileDB row idx 117) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2144( TileDB row idx 118) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2162( TileDB row idx 119) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2196( TileDB row idx 120) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2227( TileDB row idx 121) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2276( TileDB row idx 122) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2343( TileDB row idx 123) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2366( TileDB row idx 124) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2374( TileDB row idx 125) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2420( TileDB row idx 126) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2490( TileDB row idx 127) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2491( TileDB row idx 128) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2501( TileDB row idx 129) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2507( TileDB row idx 130) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2528( TileDB row idx 131) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2564( TileDB row idx 132) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2583( TileDB row idx 133) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2597( TileDB row idx 134) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2615( TileDB row idx 135) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2628( TileDB row idx 136) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2643( TileDB row idx 137) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2701( TileDB row idx 138) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2706( TileDB row idx 139) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2835( TileDB row idx 140) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV2925( TileDB row idx 141) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3029( TileDB row idx 142) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3082( TileDB row idx 143) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3125( TileDB row idx 144) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3148( TileDB row idx 145) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3165( TileDB row idx 146) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3173( TileDB row idx 147) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3186( TileDB row idx 148) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

Sample/Callset COLV3209( TileDB row idx 149) at Chromosome AKCR02000003.1 position 2272929 (TileDB column 176233601) has too many genotypes in the combined VCF record : 1081 : current limit : 1024 (num_alleles, ploidy) = (46, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),69.86073249400003,Cpu time(s),64.97854287299924

[June 30, 2022 5:00:47 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 90.10 minutes.

Runtime.totalMemory()=13059489792

java.lang.IllegalStateException: Genotype has no likelihoods: [COLI1040 TGAGC*/T GQ 39 DP 2 AD 1,1 {SB=[1, 0, 1, 0]}]

at org.broadinstitute.hellbender.utils.GenotypeUtils.computeDiploidGenotypeCounts(GenotypeUtils.java:89)

at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.calculateEH(ExcessHet.java:96)

at org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.annotate(ExcessHet.java:84)

at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:355)

at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334)

at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:306)

at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:185)

at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:135)

at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:283)

at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$null$1(VariantLocusWalker.java:161)

at java.util.Iterator.forEachRemaining(Iterator.java:116)

at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

at java.util.stream.ReferencePipeline$Head.forEachOrdered(ReferencePipeline.java:590)

at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$2(VariantLocusWalker.java:151)

at java.util.Iterator.forEachRemaining(Iterator.java:116)

at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

at java.util.stream.ReferencePipeline$Head.forEachOrdered(ReferencePipeline.java:590)

at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:148)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

(created from Zendesk ticket #290084)
gz#290084

Jul 28 '22 18:07 GATKSupportTeam

@droazen or anyone else from GATK: are you able to comment on the status of this bug, and any conversations that might be happening outside github? I posted earlier that #7962 (which is admittedly just a workaround), seems to side-step this exception. Do you foresee some other route to fix this?

Aug 08 '22 22:08 bbimber

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GenotypeGVCFs --force-output-intervals bug

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