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GATK genomicsDBImport error



  • Avatar
    Genevieve Brandt (she/her)


    In your first GenomicsDBImport command, you are getting an error:

    An index is required, but none found., for input source: file:///Users/ok/Documents/GWAS/gvcf/DA0000004922.autosome.g.vcf.gz

    You can create an index for your GVCF files with the tool IndexFeatureFile.

    Let me know how this goes for you.



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    Hello, Genevieve


    Thank you very much for telling me that I need index.

    After creating index and added interval list created by Picard VcfToIntervalList, another error occurred...

    Here's the entire code and the error


    (base) ok@SatoshinoiMac ~ %       gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \

              -V /Users/ok/Documents/GWAS/cram/DA0000004919.g.vcf.gz \

              -V /Users/ok/Documents/GWAS/cram/DA0000005016.g.vcf.gz \

              -V /Users/ok/Documents/GWAS/cram/DA0000005024.g.vcf.gz \

              -V /Users/ok/Documents/GWAS/cram/DA0000005025.g.vcf.gz \

              -V /Users/ok/Documents/GWAS/cram/DA0000005139.g.vcf.gz \

              -L /Users/ok/Documents/GWAS/cram/DA0000004919.interval_list \

          --genomicsdb-update-workspace-path /Users/ok/Documents/GWAS/mydatabase/ \

          --tmp-dir /Users/ok/tmp

    Using GATK jar /Users/ok/opt/anaconda3/pkgs/gatk4-


        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 -Xms4g -jar /Users/ok/opt/anaconda3/pkgs/gatk4- GenomicsDBImport -V /Users/ok/Documents/GWAS/cram/DA0000004919.g.vcf.gz -V /Users/ok/Documents/GWAS/cram/DA0000005016.g.vcf.gz -V /Users/ok/Documents/GWAS/cram/DA0000005024.g.vcf.gz -V /Users/ok/Documents/GWAS/cram/DA0000005025.g.vcf.gz -V /Users/ok/Documents/GWAS/cram/DA0000005139.g.vcf.gz -L /Users/ok/Documents/GWAS/cram/DA0000004919.interval_list --genomicsdb-update-workspace-path /Users/ok/Documents/GWAS/mydatabase/ --tmp-dir /Users/ok/tmp

    20:10:05.054 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/ok/opt/anaconda3/pkgs/gatk4-!/com/intel/gkl/native/libgkl_compression.dylib

    20:10:05.954 INFO  GenomicsDBImport - ------------------------------------------------------------

    20:10:05.954 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.6.1

    20:10:05.954 INFO  GenomicsDBImport - For support and documentation go to

    20:10:05.954 INFO  GenomicsDBImport - Executing as ok@SatoshinoiMac.local on Mac OS X v11.6.6 x86_64

    20:10:05.954 INFO  GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v18.0.1.1+2-6

    20:10:05.954 INFO  GenomicsDBImport - Start Date/Time: 2022年6月20日 20:10:05 JST

    20:10:05.954 INFO  GenomicsDBImport - ------------------------------------------------------------

    20:10:05.954 INFO  GenomicsDBImport - ------------------------------------------------------------

    20:10:05.955 INFO  GenomicsDBImport - HTSJDK Version: 2.24.1

    20:10:05.955 INFO  GenomicsDBImport - Picard Version: 2.27.1

    20:10:05.955 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5

    20:10:05.955 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2

    20:10:05.955 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

    20:10:05.955 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

    20:10:05.955 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

    20:10:05.955 INFO  GenomicsDBImport - Deflater: IntelDeflater

    20:10:05.955 INFO  GenomicsDBImport - Inflater: IntelInflater

    20:10:05.956 INFO  GenomicsDBImport - GCS max retries/reopens: 20

    20:10:05.956 INFO  GenomicsDBImport - Requester pays: disabled

    20:10:05.956 INFO  GenomicsDBImport - Initializing engine

    20:10:06.500 WARN  GenomicsDBImport - genomicsdb-update-workspace-path was set, so ignoring specified intervals.The tool will use the intervals specified by the initial import

    20:10:06.916 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-SNAPSHOT-6069e4a2

    20:10:06.968 INFO  GenomicsDBImport - Shutting down engine

    [2022年6月20日 20:10:06 JST] done. Elapsed time: 0.03 minutes.




    A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "/Users/ok/Documents/GWAS/cram/DA0000004919.interval_list" is not valid for this input.



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


    I'll be glad if I can get some comment on this.

    Thank you in advance 


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  • Avatar
    Genevieve Brandt (she/her)

    Hi @OK, 

    Check out this resource we have about interval lists:

    If you are using the file extension .interval_list, then the file must be in the Picard-style interval list shown in that document. 

    There are other interval list file extension options shown in that document. Once you are using a proper format and file extension, your interval list should work just fine.



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