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

GenomicsDBImport function is not executing: Aborted (core dumped)

0

2 comments

  • Avatar
    Anthony Dias-Ciarla

    Hi Tanay Biswas,

    Thank you for writing to the GATK forum. I hope that we can help you sort this out.

    After reviewing your ticket, I noticed the following issues. 

    1. You are using an outdated version of GATK. The current version is 4.2.6.1; you used an older version, 4.2.5.0.
    2. The GenomicsDBImport tool index that you linked is for an even older version of GATK than 4.2.5.0; it is from GATK version 4.0.5.2.
    3. You are not running with the correct GATK wrapper script.
    4. You are using a Panel of Normals (PON) with less than 50 samples.

    Given those issues, I strongly recommend first compiling a panel of normals with at least 50 samples. When you have those, please rerun the pipeline with the proper GATK wrapper script while using the latest version of GATK and GenomicsDBImport (4.2.6.1). Please find some additional resources below.

    Panel of Normals

    GATK4 Command-Line Syntax

    GenomicsDBImport 4.2.6.1

    I hope this helps! Please let me know if this solves your problem.

    Best,

    Anthony

    0
    Comment actions Permalink
  • Avatar
    Anthony Dias-Ciarla

    Hi Tanay Biswas,

    We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll make you a follow-up ticket to pick up where we left off.

    Thank you again for your contribution to the GATK forum!

    Best,
    Anthony

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk