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java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1

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  • Avatar
    Genevieve Brandt (she/her)

    Hi Zane Swaydan,

    I think I've found a related issue, which came up in GATK 4.2.4.0: https://github.com/broadinstitute/gatk/issues/7639 and has since been solved. Could you try creating your GenomicsDB with the most up to date GATK version?

    Let me know if that works.

    Best,

    Genevieve

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    Zane Swaydan

    Hi Genevieve,

    Thank you for your prompt reply!

    I actually changed the GenomicsDBImport version to 4.2.6.1 for a test just after the post. Here I got the logs. Unfortunately, this still does not work. Details are as follows. 

    a) GATK version used:

    GenomicsDBImport: GATK 4.2.6.1

    GenotypeGVCFs: GATK 4.2.6.1


    b) Exact command used:

    GenomicsDBImport: 

    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 -Xms2G -Xmx20G -XX:+UseParallelGC -XX:ParallelGCThreads=2 -jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenomicsDBImport --genomicsdb-workspace-path 007_Database_DBImport_VCFref/database_interval_9 --sample-name-map sample_name_map --intervals 006_IntervalsSplit_DBImport_VCFref/interval_9.list --reader-threads 5 --batch-size 60 --tmp-dir TMPDIR --max-num-intervals-to-import-in-parallel 3 --merge-input-intervals
     
    GenotypeGVCFs:
     
    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:

    GenomicsDBImport: 

    Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -Xms2G -Xmx20G -XX:+UseParallelGC -XX:ParallelGCThreads=2 -jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenomicsDBImport --genomicsdb-workspace-path 007_Database_DBImport_VCFref/database_interval_9 --sample-name-map sample_name_map --intervals 006_IntervalsSplit_DBImport_VCFref/interval_9.list --reader-threads 5 --batch-size 60 --tmp-dir TMPDIR --max-num-intervals-to-import-in-parallel 3 --merge-input-intervals
    19:16:40.098 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    19:16:40.464 INFO  GenomicsDBImport - ------------------------------------------------------------
    19:16:40.465 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.6.1
    19:16:40.465 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
    19:16:40.476 INFO  GenomicsDBImport - Executing as suizy@Pigeon on Linux v3.10.0-693.el7.x86_64 amd64
    19:16:40.476 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_161-b14
    19:16:40.476 INFO  GenomicsDBImport - Start Date/Time: June 30, 2022 7:16:40 PM CST
    19:16:40.477 INFO  GenomicsDBImport - ------------------------------------------------------------
    19:16:40.477 INFO  GenomicsDBImport - ------------------------------------------------------------
    19:16:40.478 INFO  GenomicsDBImport - HTSJDK Version: 2.24.1
    19:16:40.478 INFO  GenomicsDBImport - Picard Version: 2.27.1
    19:16:40.478 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5
    19:16:40.478 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    19:16:40.478 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    19:16:40.478 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    19:16:40.478 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    19:16:40.478 INFO  GenomicsDBImport - Deflater: IntelDeflater
    19:16:40.478 INFO  GenomicsDBImport - Inflater: IntelInflater
    19:16:40.479 INFO  GenomicsDBImport - GCS max retries/reopens: 20
    19:16:40.479 INFO  GenomicsDBImport - Requester pays: disabled
    19:16:40.479 INFO  GenomicsDBImport - Initializing engine
    19:16:42.154 INFO  IntervalArgumentCollection - Processing 21959990 bp from intervals
    19:16:42.193 INFO  GenomicsDBImport - Done initializing engine
    19:16:42.584 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a
    19:16:42.630 INFO  GenomicsDBImport - Vid Map JSON file will be written to PigeonBatch5/007_Database_DBImport_VCFref/database_interval_9/vidmap.json
    19:16:42.630 INFO  GenomicsDBImport - Callset Map JSON file will be written to PigeonBatch5/007_Database_DBImport_VCFref/database_interval_9/callset.json
    19:16:42.630 INFO  GenomicsDBImport - Complete VCF Header will be written to PigeonBatch5/007_Database_DBImport_VCFref/database_interval_9/vcfheader.vcf
    19:16:42.630 INFO  GenomicsDBImport - Importing to workspace - PigeonBatch5/007_Database_DBImport_VCFref/database_interval_9
    19:16:43.948 INFO  GenomicsDBImport - Starting batch input file preload
    19:16:53.548 INFO  GenomicsDBImport - Finished batch preload
    19:16:53.548 INFO  GenomicsDBImport - Importing batch 1 with 60 samples
    21:01:50.805 INFO  GenomicsDBImport - Done importing batch 1/3
    21:01:50.821 INFO  GenomicsDBImport - Starting batch input file preload
    21:01:55.574 INFO  GenomicsDBImport - Finished batch preload
    21:01:55.574 INFO  GenomicsDBImport - Importing batch 2 with 60 samples
    22:55:43.918 INFO  GenomicsDBImport - Done importing batch 2/3
    22:55:43.933 INFO  GenomicsDBImport - Starting batch input file preload
    22:55:46.687 INFO  GenomicsDBImport - Finished batch preload
    22:55:46.687 INFO  GenomicsDBImport - Importing batch 3 with 30 samples
    23:52:36.122 INFO  GenomicsDBImport - Done importing batch 3/3
    23:52:36.242 INFO  GenomicsDBImport - Import of all batches to GenomicsDB completed!
    23:52:36.243 INFO  GenomicsDBImport - Shutting down engine
    [June 30, 2022 11:52:36 PM CST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 275.94 minutes.
    Runtime.totalMemory()=5605687296
    Tool returned:
    true

    GenotypeGVCFs:

    Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -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
    23:52:49.781 info  NativeGenomicsDB - pid=156006 tid=156007 No valid combination operation found for INFO field DS  - the field will NOT be part of INFO fields in the generated VCF records
    23:52:49.781 info  NativeGenomicsDB - pid=156006 tid=156007 No valid combination operation found for INFO field HaplotypeScore  - the field will NOT be part of INFO fields in the generated VCF records
    23:52:49.781 info  NativeGenomicsDB - pid=156006 tid=156007 No valid combination operation found for INFO field InbreedingCoeff  - the field will NOT be part of INFO fields in the generated VCF records
    23:52:49.781 info  NativeGenomicsDB - pid=156006 tid=156007 No valid combination operation found for INFO field MLEAC  - the field will NOT be part of INFO fields in the generated VCF records
    23:52:49.781 info  NativeGenomicsDB - pid=156006 tid=156007 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),87.87669125599962,Cpu time(s),60.40666510100034
    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),71.34584674099888,Cpu time(s),64.20573086500079
    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),74.14547183399837,Cpu time(s),67.38693261000097
    [July 1, 2022 1:36:56 AM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 104.22 minutes.
    Runtime.totalMemory()=13973323776
    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)
    0
    Comment actions Permalink
  • Avatar
    Anthony Dias-Ciarla

    Hi Zane Swaydan,

    Thank you for writing to the GATK forum! We hope that we can help you get this sorted out.

    Our first suggestion is to try re-running GenotypeGVCFs with --max-genotype-count set to a value greater than 1024; this should prevent the PLs from getting dropped and will avoid the downstream error. You may also need to increase --max-alternate-alleles as well.

    Additionally, it would be helpful if you could confirm whether the tool successfully runs if you omit the --force-output-intervals argument?

    Please give the above a try and let us know what you get!

    Best,
    Anthony

    0
    Comment actions Permalink
  • Avatar
    Zane Swaydan

    Hi Anthony Dias-Ciarla,

    Thank you for your suggestion! I did some further tests and still have some problems here.

    When I use "--max-genotype-count 200 --genomicsdb-max-alternate-alleles 1201 --max-alternate-alleles 1200" in GenotypeGVCFs, jobs with "--force-output-intervals" always failed. But jobs without "--force-output-intervals" finished successfully:

    # With "--force-output-intervals"

    Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -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 --max-genotype-count 200 --genomicsdb-max-alternate-alleles 1201 --max-alternate-alleles 1200 --allow-old-rms-mapping-quality-annotation-data --only-output-calls-starting-in-intervals --verbosity ERROR

    14:11:55.265 info NativeGenomicsDB - pid=174178 tid=174180 No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records

    14:11:55.265 info NativeGenomicsDB - pid=174178 tid=174180 No valid combination operation found for INFO field HaplotypeScore - the field will NOT be part of INFO fields in the generated VCF records

    14:11:55.265 info NativeGenomicsDB - pid=174178 tid=174180 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records

    14:11:55.265 info NativeGenomicsDB - pid=174178 tid=174180 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records

    14:11:55.265 info NativeGenomicsDB - pid=174178 tid=174180 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),93.78461034100029,Cpu time(s),49.63175313099868

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),76.34317971699944,Cpu time(s),53.71619038400103

    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 : 200 (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 : 200 (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 : 200 (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.

    <---------- Similar lines are omitted ---------->

    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 : 200 (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 : 200 (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 : 200 (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),75.95020304200023,Cpu time(s),52.549281510000625

    [July 20, 2022 4:04:59 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 113.16 minutes.

    Runtime.totalMemory()=13022789632

    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)

     
    # Without "--force-output-intervals"

    Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -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 -V gendb://007_Database_DBImport_VCFref/database_interval_9 -O 008_RawVcfGz_DBImport_VCFref/001_DividedIntervals/interval_9.vcf.gz --tmp-dir TMPDIR --max-genotype-count 200 --genomicsdb-max-alternate-alleles 1201 --max-alternate-alleles 1200 --allow-old-rms-mapping-quality-annotation-data --only-output-calls-starting-in-intervals --verbosity ERROR

    18:48:51.266 info NativeGenomicsDB - pid=181881 tid=181884 No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records

    18:48:51.266 info NativeGenomicsDB - pid=181881 tid=181884 No valid combination operation found for INFO field HaplotypeScore - the field will NOT be part of INFO fields in the generated VCF records

    18:48:51.266 info NativeGenomicsDB - pid=181881 tid=181884 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records

    18:48:51.266 info NativeGenomicsDB - pid=181881 tid=181884 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records

    18:48:51.266 info NativeGenomicsDB - pid=181881 tid=181884 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records

    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 : 200 (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 : 200 (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 : 200 (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 : 200 (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.

    <---------- Similar lines are omitted ---------->

    Sample/Callset COLV3173( TileDB row idx 147) at Chromosome AKCR02000003.1 position 22621153 (TileDB column 196581825) has too many genotypes in the combined VCF record : 528 : current limit : 200 (num_alleles, ploidy) = (32, 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 22621153 (TileDB column 196581825) has too many genotypes in the combined VCF record : 528 : current limit : 200 (num_alleles, ploidy) = (32, 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 22621153 (TileDB column 196581825) has too many genotypes in the combined VCF record : 528 : current limit : 200 (num_alleles, ploidy) = (32, 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),7669.852204786199,Cpu time(s),6588.393799889893

    [July 20, 2022 11:07:46 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 259.27 minutes.

    Runtime.totalMemory()=7657226240


    But when I use "--max-genotype-count 1200 --genomicsdb-max-alternate-alleles 1201 --max-alternate-alleles 1200" in GenotypeGVCFs, jobs with "--force-output-intervals" finished successfully:

    # With "--force-output-intervals"

    Using GATK jar MySoftwares/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -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 -V gendb://007_Database_DBImport_VCFref/database_interval_9 -O 008_RawVcfGz_DBImport_VCFref/001_DividedIntervals/interval_9.vcf.gz --tmp-dir TMPDIR --max-genotype-count 1200 --genomicsdb-max-alternate-alleles 1201 --max-alternate-alleles 1200 --force-output-intervals PigeonBatch4/008_RawVcfGz/MergeVcf/pigeonBatch1234_filtered.vcf.gz --allow-old-rms-mapping-quality-annotation-data --only-output-calls-starting-in-intervals --verbosity ERROR

    10:09:05.432 info NativeGenomicsDB - pid=73656 tid=73657 No valid combination operation found for INFO field DS - the field will NOT be part of INFO fields in the generated VCF records

    10:09:05.432 info NativeGenomicsDB - pid=73656 tid=73657 No valid combination operation found for INFO field HaplotypeScore - the field will NOT be part of INFO fields in the generated VCF records

    10:09:05.432 info NativeGenomicsDB - pid=73656 tid=73657 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records

    10:09:05.432 info NativeGenomicsDB - pid=73656 tid=73657 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records

    10:09:05.432 info NativeGenomicsDB - pid=73656 tid=73657 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),89.44181804899745,Cpu time(s),63.4057867389993

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.66081742700032,Cpu time(s),61.15157077800037

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.73530727900004,Cpu time(s),64.28787743200058

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),68.31645824200008,Cpu time(s),64.37346404600076

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.80634287200083,Cpu time(s),62.99494451999987

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.88407319400038,Cpu time(s),62.41153228300053

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),63.53221452800035,Cpu time(s),60.54694494200093

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.62165783599947,Cpu time(s),61.565376386000345

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.75127961500112,Cpu time(s),63.12102589299974

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),75.33344563999995,Cpu time(s),72.87375666899906

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),69.99621136199944,Cpu time(s),65.41662833499939

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),69.89269830700015,Cpu time(s),67.88472582399933

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.77105792099908,Cpu time(s),60.574865439999904

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.705994199999594,Cpu time(s),59.919269467999364

    Sample/Callset COLI0776( TileDB row idx 0) at Chromosome AKCR02000003.1 position 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 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 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 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 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

    <---------- Similar lines are omitted ---------->

    Sample/Callset COLV3173( TileDB row idx 147) at Chromosome AKCR02000003.1 position 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 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 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 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 4690814 (TileDB column 178651486) has too many genotypes in the combined VCF record : 2016 : current limit : 1200 (num_alleles, ploidy) = (63, 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),68.84224669800099,Cpu time(s),65.11545287999813

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),69.15679926400018,Cpu time(s),64.397888132

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),63.97428030200008,Cpu time(s),61.679740540999916

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.92642611799988,Cpu time(s),64.16524851699954

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),68.18919311100038,Cpu time(s),64.92547050499923

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.52267019399855,Cpu time(s),62.73946082799948

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),69.18523070599907,Cpu time(s),65.90385215000148

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.74469262300097,Cpu time(s),63.886654410001206

    Sample/Callset COLI0776( TileDB row idx 0) at Chromosome AKCR02000003.1 position 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

    <---------- Similar lines are omitted ---------->

    Sample/Callset COLV3173( TileDB row idx 147) at Chromosome AKCR02000003.1 position 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 6305085 (TileDB column 180265757) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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),64.9151755270008,Cpu time(s),60.67419706099999

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.71294428000004,Cpu time(s),62.15501877399976

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.89663066200089,Cpu time(s),61.51919565000072

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),73.22093742700226,Cpu time(s),62.21752029100043

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.19757446500078,Cpu time(s),62.33634354899985

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.89084249900023,Cpu time(s),65.17698133599978

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.52768320799925,Cpu time(s),63.806871953000126

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.62247870699993,Cpu time(s),62.762701058998964

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),68.89931507000117,Cpu time(s),66.26757393900138

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.55920078300095,Cpu time(s),60.66927491199952

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.83427225599989,Cpu time(s),62.399661456999866

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.21460389899945,Cpu time(s),56.52457334599994

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),72.0843924950011,Cpu time(s),61.896373012001504

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),63.355789102000784,Cpu time(s),62.06728500200117

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.66849613600026,Cpu time(s),64.78834016299999

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.92398467799961,Cpu time(s),64.46466597799984

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.58884600500068,Cpu time(s),62.5757328590001

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.81794315699959,Cpu time(s),61.875247516999515

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.29076345599876,Cpu time(s),60.35241777900041

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.35728984000015,Cpu time(s),62.481517170001595

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.08223507299904,Cpu time(s),63.44127452000201

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.21018233300016,Cpu time(s),64.89229681799951

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.3450305879993,Cpu time(s),65.64214584699984

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),70.95695521799999,Cpu time(s),65.30823301499943

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.93665805500031,Cpu time(s),61.43388086399931

    Sample/Callset COLI0776( TileDB row idx 0) at Chromosome AKCR02000003.1 position 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 2). Fields, such as PL, with length equal to the number of genotypes will NOT be added for this sample for this location.

    <---------- Similar lines are omitted ---------->

    Sample/Callset COLV3173( TileDB row idx 147) at Chromosome AKCR02000003.1 position 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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 11213317 (TileDB column 185173989) has too many genotypes in the combined VCF record : 1326 : current limit : 1200 (num_alleles, ploidy) = (51, 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),68.99746954600036,Cpu time(s),65.22786611400022

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),63.74769623300003,Cpu time(s),60.021282834000736

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.77022901300121,Cpu time(s),62.89875949599873

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.43312615099995,Cpu time(s),61.82574154899916

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.83256013500015,Cpu time(s),60.815705952000336

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.4628585290006,Cpu time(s),61.7233711949999

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),64.46399785600003,Cpu time(s),60.922775742999455

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.77097971499931,Cpu time(s),61.23645004599928

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.30628528,Cpu time(s),53.54422893199969

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),58.66944537800087,Cpu time(s),49.75495243900087

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.427944533000854,Cpu time(s),56.46845883299872

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.297417327000865,Cpu time(s),59.605855965000195

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.566034745999296,Cpu time(s),53.27913427200064

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),48.68708143399968,Cpu time(s),47.31631521500023

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),49.97562844100035,Cpu time(s),48.16521321600002

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),54.87174862800101,Cpu time(s),51.28670147299941

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),52.92515456499985,Cpu time(s),51.06284728799986

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.16354027000032,Cpu time(s),54.765510589000264

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.94832259800003,Cpu time(s),51.92831399299971

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),61.38867754800091,Cpu time(s),50.724426352000634

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.574163157999834,Cpu time(s),54.409659977000246

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),54.19717660300003,Cpu time(s),52.14061926899986

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),52.68216496899902,Cpu time(s),51.12456371999856

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.615056506000016,Cpu time(s),53.09996186899969

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.851704093001345,Cpu time(s),52.215127561999495

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.17736226300019,Cpu time(s),51.040865108999704

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.7498998620002,Cpu time(s),55.306191478999175

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.924260178999766,Cpu time(s),53.412536695000234

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.86271386899916,Cpu time(s),55.13334703299968

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),66.29449385599901,Cpu time(s),57.406513519000065

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.687347780000614,Cpu time(s),55.722990134999996

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.49026945399925,Cpu time(s),53.406372032999876

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.480705132000274,Cpu time(s),55.178488470998786

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),58.93179678100007,Cpu time(s),56.485911123001486

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.218052469999115,Cpu time(s),52.372007606000075

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.842120128999085,Cpu time(s),55.37829730799895

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.85721867500121,Cpu time(s),52.13027602399953

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),65.8066660259998,Cpu time(s),55.961807774000626

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),58.25801225600066,Cpu time(s),54.681550040000104

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.498143036999444,Cpu time(s),54.85646790899963

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.06448303400004,Cpu time(s),53.540987805000114

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.817220832000174,Cpu time(s),54.62421347599958

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.32965768299969,Cpu time(s),53.05130843000039

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),60.64715788600033,Cpu time(s),55.8243726630005

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.32419357400028,Cpu time(s),56.9181709290004

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.15130770499799,Cpu time(s),56.88707543099948

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.88109758699947,Cpu time(s),53.622476786999634

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),54.78644105300081,Cpu time(s),52.008759018999946

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.63367849899952,Cpu time(s),54.045042009000504

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.732167340000196,Cpu time(s),54.52438792500029

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),56.74357819700014,Cpu time(s),54.12580988799975

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.41612004000062,Cpu time(s),53.189125769000306

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.89609942700004,Cpu time(s),54.70539873199982

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),55.8086095850004,Cpu time(s),54.078571822999756

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.01961282199969,Cpu time(s),55.32276895799888

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),62.89527058299923,Cpu time(s),57.565639643999276

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),58.69566790800085,Cpu time(s),54.72756563700032

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),60.22289228500072,Cpu time(s),56.12973052100078

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),57.41269357599955,Cpu time(s),53.93796219500013

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),58.93321488100058,Cpu time(s),54.89717103899983

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),67.00297054000083,Cpu time(s),55.63939561299957

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),59.63857013699922,Cpu time(s),57.18620689799968

    GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),45.89393978499981,Cpu time(s),43.9104061679996

    [July 21, 2022 6:37:36 PM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 508.63 minutes.

    Runtime.totalMemory()=16515072000


    So it seems that this "IllegalStateException" issue is associated with both "--max-genotype-count" and "--force-output-intervals". I am still confused about this...

    What's more, I also tried replacing "GenomicsDBImport" with "CombineGVCFs" in my pipeline. The following "GenotypeGVCFs" with "--force-output-intervals" runs without error reports.
     
    Using GATK jar MySoftwares/gatk-4.2.4.0/gatk-package-4.2.4.0-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 -Xms4G -Xmx16G -XX:+UseParallelGC -XX:ParallelGCThreads=2 -jar MySoftwares/gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar GenotypeGVCFs -R PigeonBatch5/000_DataLinks/000_RefSeq/Cliv2.1_genomic.fasta --force-output-intervals PigeonBatch4/008_RawVcfGz/MergeVcf/pigeonBatch1234_filtered.vcf.gz -ip 100 -V 007_MrgdGVCF_combineGVCF_VCFref/interval_9.g.vcf.gz -O 008_RawVcfGz_combineGVCF_VCFref/001_DividedIntervals/interval_9.vcf.gz --tmp-dir TMPDIR --allow-old-rms-mapping-quality-annotation-data --verbosity ERROR

    [July 3, 2022 6:24:01 AM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 309.62 minutes.

    Runtime.totalMemory()=16559112192
     
    But in the VCF result, I found that locus in "--force-output-intervals" are likely to be given more missing genotypes. When I merged "GenotypeGVCFs --force-output-intervals" output VCF with "--force-output-intervals" reference VCF (which is a fully joint-called result), samples in "GenotypeGVCFs --force-output-intervals" output VCF have significantly higher missing rate according to "vcftools --missing-indv" (sequencing depth and pre-processes are similar). I'm inquisitive if this is normal.
     
    Thanks again for your help!
     
    Best,
    Zane
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    Anthony Dias-Ciarla

    Hi Zane Swaydan,

    Thank you for following up with this information!

    There does seem to be a bug in the --force-output-intervals of GenotypeGVCFs. Contrarily, the issue when changing --max-genotype-count is not a bug that needs fixing. You must ensure you select options properly when making such changes. It is not surprising that --max-genotype-count triggers this bug, but the main bug seems to be with --force-output-intervals. Our developers are looking further into this.

    In your last paragraph, you cite missing genotype data; this is normal with --force-output-intervals. Since --force-output-intervals primary function is to force output, it will indeed "force" the display of missing data if no data is present. To avoid seeing this missing data, run without --force-output-intervals.

    Additionally, GenomicsDB drops PLs; if you change the caps, it can change whether or not records will exist without PLs.

    Below are some suggestions for moving forward.

    1. Please use the most updated version of GATK (4.2.6.1). It seems you are running the 4.2.4.0 version in addition to the newest version. Please use the latest version for all of your analyses.
    2. Omit the use of --force-output-intervals to avoid triggering the bug.
    3. If you do not mind the slower speed, you can keep running CombineGVCFs since GenomicsDB is what is dropping the PLs.

    I hope this provides some clarity and viable next steps! Be sure to let me know if they work out. I will keep you up to date with any further updates.

    Best,

    Anthony

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    Zane Swaydan

    Hi Anthony Dias-Ciarla,

    Thank you for your explanation and your team for working hard on this! 

    I'm working on extracting intervals in "--force-output-intervals" with padding regions as separate "pseudo-chromosomes" and re-run the analysis with "pseudo-genome" without "--force-output-intervals". It seems to work fine since I can acquire genotypes at a much lower missing rate, but I'm still concerned about the probable issues of this DIY method. 

    Thanks again for your help! I'll keep following up if there is any progress here! ;)

    Best,

    Zane

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    Anthony Dias-Ciarla

    Hi Zane Swaydan,

    Thank you for following up! I want to make you aware of a GitHub ticket I created for this issue. I’ve included the link below so you can follow along with the progress as the developers search for answers.

    GitHub Ticket #7966

    I hope this helps! Please feel free to reach out at any time if further questions arise.

    Best,

    Anthony

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    Zane Swaydan

    Hi Anthony Dias-Ciarla,

    Link received, thank you! Let me know if you need more information about this issue! 

    Best,

    Zane

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