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

JointGenotyping.ImportGvcfs terminates without an active exception

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    Anthony Dias-Ciarla

    Hi Elizabeth Lee,

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

    I brought this to our developers and received some feedback to share. Firstly, they would like to know if you can see any output after the GenomicsDBImport run completes? The issue appears to be occurring after the tool finishes its run and tries to shut down.

    Try running SelectVariants in the GenomicsDBImport. This appears to be a bug in the GenomicsDBImport code. I have created a GitHub ticket and tagged our GenomicsDBImport team members to help you going forward.

    Please find the link to the GitHub ticket here. You can follow along with all progress there. I'm confident that our team will be able to help you solve this as soon as possible. If you have any other questions in the meantime, please do not hesitate to reach out.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Elizabeth Lee,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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    Anthony Dias-Ciarla

    Hi Elizabeth Lee,

    As promised, I pinged our developers to see if they had any additional questions and feedback for you.

    Upon further review, it appears that it is not a bug with GenomicsDBImport; the problem seems to originate from your environment. Can you try running GenomicsDBImport with Docker instead of Singularity? Do you have a workaround? Is this repeatable? Have you run this on separate days with the same commands and had it fail the same way?

    Regrettably, we do not support or have much familiarity with Singularity, but we do support issues with Docker (containers - image - registry) and Google Cloud. So if you re-run with Docker and encounter the same problem, we may be better equipped and able to help you troubleshoot.

    Thank you for being a valued contributor to the GATK community! We hope to hear back from you soon. In the meantime, please do not hesitate to reach out if any other questions arise.

    Best,

    Anthony

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    Anthony Dias-Ciarla

    Hi Elizabeth Lee,

    We haven't heard from you for a while, so we will close this GATK forum ticket internally. However, this forum thread will remain open, along with your GitHub ticket. If you still require assistance or have further updates to my last reply, you only need to respond to this email, and we'll re-open your ticket and would be more than happy to pick up where we left off! 

    Kind regards,

    Anthony​

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