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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

CalculateGenotypePosteriors Follow

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    Kshama Aswath

    Hi ,

    I get this error when I use supporting population. If I run without it then it works. IS this coz my vcf input is a multisample input or is it some other reason? 

    Using GATK jar /usr/local/apps/GATK/


        java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /usr/local/apps/GATK/ CalculateGenotypePosteriors -V all_jointcalls_sRecal_allPASS.vcf -supporting 1000G_subset_phase1.snps.high_confidence.hg38.vcf.gz -O all_jointcalls_sRecal_allPASS_PP1000G.vcf --skip-family-priors

    16:34:39.706 INFO  NativeLibraryLoader - Loading from jar:file:/usr/local/apps/GATK/!/com/intel/gkl/native/

    Sep 16, 2020 4:34:40 PM runningOnComputeEngine

    INFO: Failed to detect whether we are running on Google Compute Engine.

    16:34:40.047 INFO  CalculateGenotypePosteriors - ------------------------------------------------------------

    16:34:40.047 INFO  CalculateGenotypePosteriors - The Genome Analysis Toolkit (GATK) v4.1.8.0

    16:34:40.047 INFO  CalculateGenotypePosteriors - For support and documentation go to

    16:34:40.048 INFO  CalculateGenotypePosteriors - Executing as aswathk@cn2969 on Linux v3.10.0-862.14.4.el7.x86_64 amd64

    16:34:40.048 INFO  CalculateGenotypePosteriors - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-b13

    16:34:40.048 INFO  CalculateGenotypePosteriors - Start Date/Time: September 16, 2020 4:34:39 PM EDT

    16:34:40.048 INFO  CalculateGenotypePosteriors - ------------------------------------------------------------

    16:34:40.048 INFO  CalculateGenotypePosteriors - ------------------------------------------------------------

    16:34:40.049 INFO  CalculateGenotypePosteriors - HTSJDK Version: 2.22.0

    16:34:40.049 INFO  CalculateGenotypePosteriors - Picard Version: 2.22.8

    16:34:40.049 INFO  CalculateGenotypePosteriors - HTSJDK Defaults.COMPRESSION_LEVEL : 2

    16:34:40.050 INFO  CalculateGenotypePosteriors - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

    16:34:40.050 INFO  CalculateGenotypePosteriors - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

    16:34:40.050 INFO  CalculateGenotypePosteriors - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

    16:34:40.050 INFO  CalculateGenotypePosteriors - Deflater: IntelDeflater

    16:34:40.050 INFO  CalculateGenotypePosteriors - Inflater: IntelInflater

    16:34:40.050 INFO  CalculateGenotypePosteriors - GCS max retries/reopens: 20

    16:34:40.050 INFO  CalculateGenotypePosteriors - Requester pays: disabled

    16:34:40.051 INFO  CalculateGenotypePosteriors - Initializing engine

    16:34:40.420 INFO  FeatureManager - Using codec VCFCodec to read file file:///gpfs/gsfs12/users/aswathk/hpc_readgroups_1/RD_bams/markduplicates_bams/bqsr_all/all_vcf/GATK_resourcebundle/1000G_subset_phase1.snps.high_confidence.hg38.vcf.gz

    16:34:40.668 INFO  FeatureManager - Using codec VCFCodec to read file file:///gpfs/gsfs12/users/aswathk/hpc_readgroups_1/RD_bams/markduplicates_bams/bqsr_all/all_vcf/GATK_resourcebundle/all_jointcalls_sRecal_allPASS.vcf

    16:34:41.065 INFO  CalculateGenotypePosteriors - Done initializing engine

    16:34:41.289 INFO  ProgressMeter - Starting traversal

    16:34:41.289 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

    16:34:42.911 INFO  CalculateGenotypePosteriors - Shutting down engine

    [September 16, 2020 4:34:42 PM EDT] done. Elapsed time: 0.05 minutes.




    A USER ERROR has occurred: Variant does not contain the same number of MLE allele counts as alternate alleles for record at chr2:114704



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


    I tried looking up this MLE using vcftools and here is what I got.

    Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    Can this be an issue that GATK is throwing a fit? 

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