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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

erro NativeGenomicsDB - pid=26649 tid=26687 conflicting field description in the vid JSON and the VCF header of file:

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    Genevieve Brandt

    Hello Hind Fakhri, please post your complete stack trace so we can look into the error.

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    Hind Fakhri

    yes @Genevieve Brandt

    [hnoureldin@kcn496 NovaSeq]$ /app/Genome/gatk-4.1.8.1/gatk GenomicsDBImport -V PBG-956-20_S2.genome.vcf.gz -V PBG-957-20_S3.genome.vcf.gz --genomicsdb-workspace-path genomicBD2 --java-options "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" -L chr17:41197577-41276148
    Using GATK jar /app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-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 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar GenomicsDBImport -V PBG-956-20_S2.genome.vcf.gz -V PBG-957-20_S3.genome.vcf.gz --genomicsdb-workspace-path genomicBD2 -L chr17:41197577-41276148
    13:20:44.817 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/app/Genome/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Oct 08, 2020 1:20:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    13:20:45.016 INFO GenomicsDBImport - ------------------------------------------------------------
    13:20:45.016 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.8.1
    13:20:45.017 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
    13:20:45.017 INFO GenomicsDBImport - Executing as hnoureldin@kcn496 on Linux v2.6.32-358.23.2.el6.x86_64 amd64
    13:20:45.017 INFO GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_66-b17
    13:20:45.017 INFO GenomicsDBImport - Start Date/Time: October 8, 2020 1:20:44 PM AST
    13:20:45.017 INFO GenomicsDBImport - ------------------------------------------------------------
    13:20:45.017 INFO GenomicsDBImport - ------------------------------------------------------------
    13:20:45.018 INFO GenomicsDBImport - HTSJDK Version: 2.23.0
    13:20:45.018 INFO GenomicsDBImport - Picard Version: 2.22.8
    13:20:45.018 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    13:20:45.018 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    13:20:45.018 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    13:20:45.018 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    13:20:45.018 INFO GenomicsDBImport - Deflater: IntelDeflater
    13:20:45.018 INFO GenomicsDBImport - Inflater: IntelInflater
    13:20:45.018 INFO GenomicsDBImport - GCS max retries/reopens: 20
    13:20:45.018 INFO GenomicsDBImport - Requester pays: disabled
    13:20:45.018 INFO GenomicsDBImport - Initializing engine
    13:20:45.451 INFO IntervalArgumentCollection - Processing 78572 bp from intervals
    13:20:45.452 INFO GenomicsDBImport - Done initializing engine
    13:20:45.789 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.0-e701905
    13:20:45.792 INFO GenomicsDBImport - Vid Map JSON file will be written to /fefs1/Genome/hnoureldin/201001/NovaSeq/genomicBD2/vidmap.json
    13:20:45.792 INFO GenomicsDBImport - Callset Map JSON file will be written to /fefs1/Genome/hnoureldin/201001/NovaSeq/genomicBD2/callset.json
    13:20:45.792 INFO GenomicsDBImport - Complete VCF Header will be written to /fefs1/Genome/hnoureldin/201001/NovaSeq/genomicBD2/vcfheader.vcf
    13:20:45.793 INFO GenomicsDBImport - Importing to workspace - /fefs1/Genome/hnoureldin/201001/NovaSeq/genomicBD2
    13:20:45.793 INFO ProgressMeter - Starting traversal
    13:20:45.793 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
    13:20:45.940 INFO GenomicsDBImport - Importing batch 1 with 2 samples
    13:20:45.971 erro NativeGenomicsDB - pid=28428 tid=28466 conflicting field description in the vid JSON and the VCF header of file: PBG-956-20_S2.bam_stream
    terminate called after throwing an instance of 'std::exception'
    what(): std::exception

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    Genevieve Brandt

    Hello Hind Fakhri, we just released GATK 4.1.9.0 and there is an improvement in the GenomicsDB error message to determine more information about these issues. Please re-run with that version and post your stack trace so we can look into it.

    We also had a similar issue discussed on the forum that was solved, please see the post for troubleshooting ideas: https://gatk.broadinstitute.org/hc/en-us/community/posts/360073153571-GenomicsDBImport-failing-on-conflicting-field-description-

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