Genome Analysis Toolkit

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

libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow

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    Anthony Dias-Ciarla

    Hi Marta Giovalli,

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

    When reviewing your inquiry, a couple of things stand out to me as potential problems. The version of GATK you are using (4.1.0.0) and the source of your GATK Best Practices Workflow seem to be the origin of the issue at first glance. 

    Here are some suggestions on things to try first:

    1. Update to the latest version of GATK (4.2.6.1)
    2. Follow the Germline short variant discovery (SNPs and Indels) Best Practices Workflow directly from our website.

    I hope this helps! Please let me know whether or not this leads you to success. If not, I can take this to our developers for a closer look. If any other questions arise in the meantime, please do not hesitate to reach out.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Marta Giovalli,

    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 create a follow-up ticket to pick up where we left off.

    Thank you again for contributing to our GATK forum!

    Best,

    Anthony

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    Marta Giovalli

    Updating to the latest version of GATK (4.2.6.1) did the trick.

    Thank you!

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    Genevieve Brandt (she/her)

    Thank you for posting the solution Marta Giovalli!

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