Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

GATK genomicsDBImport error

Answered
Follow
Avatar
@OK

REQUIRED for all errors and issues:
a) GATK version used:

gatk4.2.6.1

HTSJDK 2.24.1

Picard 2.27.1

b) Exact command used:

      gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \

  -V /Users/ok/Documents/GWAS/gvcf/DA0000004922.autosome.g.vcf.gz \

  -V /Users/ok/Documents/GWAS/gvcf/DA0000004938.autosome.g.vcf.gz \

  -V /Users/ok/Documents/GWAS/gvcf/DA0000005086.autosome.g.vcf.gz \

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

      --tmp-dir /Users/ok/tmp \

 

  gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport \

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

      --output-interval-list-to-file /Users/ok/Documents/GWAS/gvcf

c) Entire program log:

  

 

  Using GATK jar /Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/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 -Xmx4g -Xms4g -jar /Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar GenomicsDBImport -V /Users/ok/Documents/GWAS/gvcf/DA0000004922.autosome.g.vcf.gz -V /Users/ok/Documents/GWAS/gvcf/DA0000004938.autosome.g.vcf.gz -V /Users/ok/Documents/GWAS/gvcf/DA0000005086.autosome.g.vcf.gz --genomicsdb-update-workspace-path /Users/ok/Documents/GWAS/gvcf --tmp-dir /Users/ok/tmp

19:47:47.550 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.dylib

19:47:47.945 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:47.945 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.6.1

19:47:47.945 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/

19:47:47.945 INFO  GenomicsDBImport - Executing as ok@SatoshinoiMac.local on Mac OS X v11.6.6 x86_64

19:47:47.945 INFO  GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v18.0.1.1+2-6

19:47:47.945 INFO  GenomicsDBImport - Start Date/Time: 2022年6月14日 19:47:47 JST

19:47:47.945 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:47.945 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:47.946 INFO  GenomicsDBImport - HTSJDK Version: 2.24.1

19:47:47.946 INFO  GenomicsDBImport - Picard Version: 2.27.1

19:47:47.946 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5

19:47:47.946 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2

19:47:47.946 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

19:47:47.946 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

19:47:47.946 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

19:47:47.946 INFO  GenomicsDBImport - Deflater: IntelDeflater

19:47:47.946 INFO  GenomicsDBImport - Inflater: IntelInflater

19:47:47.946 INFO  GenomicsDBImport - GCS max retries/reopens: 20

19:47:47.946 INFO  GenomicsDBImport - Requester pays: disabled

19:47:47.946 INFO  GenomicsDBImport - Initializing engine

19:47:47.998 INFO  GenomicsDBImport - Shutting down engine

[2022年6月14日 19:47:47 JST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=4294967296

***********************************************************************

 

A USER ERROR has occurred: Failed to create reader from file:///Users/ok/Documents/GWAS/gvcf/DA0000004922.autosome.g.vcf.gz because of the following error:

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

 

***********************************************************************

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

Using GATK jar /Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/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 -Xmx4g -Xms4g -jar /Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar GenomicsDBImport --genomicsdb-update-workspace-path /Users/ok/Documents/GWAS/gvcf --output-interval-list-to-file /Users/ok/Documents/GWAS/gvcf

19:47:54.390 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.dylib

19:47:54.555 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:54.555 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.6.1

19:47:54.555 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/

19:47:54.555 INFO  GenomicsDBImport - Executing as ok@SatoshinoiMac.local on Mac OS X v11.6.6 x86_64

19:47:54.555 INFO  GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v18.0.1.1+2-6

19:47:54.556 INFO  GenomicsDBImport - Start Date/Time: 2022年6月14日 19:47:54 JST

19:47:54.556 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:54.556 INFO  GenomicsDBImport - ------------------------------------------------------------

19:47:54.556 INFO  GenomicsDBImport - HTSJDK Version: 2.24.1

19:47:54.556 INFO  GenomicsDBImport - Picard Version: 2.27.1

19:47:54.556 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5

19:47:54.556 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2

19:47:54.556 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

19:47:54.556 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

19:47:54.557 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

19:47:54.557 INFO  GenomicsDBImport - Deflater: IntelDeflater

19:47:54.557 INFO  GenomicsDBImport - Inflater: IntelInflater

19:47:54.557 INFO  GenomicsDBImport - GCS max retries/reopens: 20

19:47:54.557 INFO  GenomicsDBImport - Requester pays: disabled

19:47:54.557 INFO  GenomicsDBImport - Initializing engine

19:47:54.558 INFO  GenomicsDBImport - Shutting down engine

[2022年6月14日 19:47:54 JST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=4294967296

***********************************************************************

 

A USER ERROR has occurred: Couldn't read file file:///Users/ok/Documents/GWAS/gvcf/vcfheader.vcf. Error was: It doesn't exist.

 

***********************************************************************

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

 

 

Hello, 

I'm working on merging the multiple gvcf files to jointgenotype.

However, when I tried to produce intervalList, the above-mentioned error had occurred.

I am glad if someone know how it occur.

Thank you in advance.

0

3 comments

Sort by Date Votes
  • Avatar
    Genevieve Brandt (she/her)

    Hello,

    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.

    Best,

    Genevieve

    1
    Comment actions Permalink
  • Avatar
    @OK

    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/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/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 -Xmx4g -Xms4g -jar /Users/ok/opt/anaconda3/pkgs/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar 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/gatk4-4.2.6.1-py36hdfd78af_1/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar!/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 https://software.broadinstitute.org/gatk/

    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] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.03 minutes.

    Runtime.totalMemory()=4294967296

    ***********************************************************************

     

    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 

    @OK

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Hi @OK, 

    Check out this resource we have about interval lists: https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-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.

    Best,

    Genevieve

    0
    Comment actions Permalink

Please sign in to leave a comment.

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You Post

Get Email Notifications

Didn't find what you were looking for?

New post

Quick Links

GATK Latest Releases

Known Issues & Troubleshooting

Submitting a Bug Report

How to Track a Github issue

GATK on the Cloud with Terra

Recent GATK News

GATK Blog Posts

GATK Twitter Page

About the GATK community

  • 133,119 Total Users
  • 0 Comments
  • 0 Posts
  • 0 Votes
Powered by Zendesk