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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

[Funcotator] java.lang.IllegalArgumentException: Unexpected value: lncRNA

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8 comments

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    Samantha (she/her)

    Hi sahuno,

     

    Thanks for writing in. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace?

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

     

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Thanks,

    Samantha

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    sahuno

    Hi Samantha-she-her

    I've added ` GROUP_FireCloud-Support@firecloud.org ` to the current workspace and sent submission details  to email.

    could you please confirm you have it?

     

    Kind regards

    SA

     

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    Samantha (she/her)

    Hi sahuno,

     

    Confirming I received your email, thank you for sending that information over. I will take a look and get back to you.

     

    Best,

    Samantha

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    Samantha (she/her)

    Hi sahuno,

     

    It looks like the issue may have been that the GATK docker you were using was a different version than the workflow you were running (4.1.8.1 vs 4.1.7.0). I've noticed that you recently ran the workflow again with GATK 4.1.7.0 and the submission was successful. It looks like you've solved the issue on your own, but if you need any further assistance, please let me know.

     

    Best,

    Samantha

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    sahuno

    Hi Samantha-she-her 

    I appreciate your time looking at the workflow and logs. You are right about conflicts in gatk docker versions in workflow and as attribute I specified.

    but i I don't think alignment of gatk docker version to `4.1.7.0` was the only issue for the error;

    java.lang.IllegalArgumentException: Unexpected value: lncRNA

    You could see that when i used gatk docker `4.1.7.0` with latest functotator datasource it failed (Submission ID- 226cc74b-46aa-4ccf-bca3-d1ac61fe8877)

    Rather downgrading the Funcotator datasource  used in the workflow from funcotator_dataSources.v1.7.20200521s.tar.gz to funcotator_dataSources.v1.6.20190124s.tar.gz helped. 

     

    or maybe I'm not doing something right again?

     

    Kind regards
    Sam

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    Samantha (she/her)

    Hi sahuno,

     

    It looks like what you are experiencing is a known issue with funcotator_dataSources.v1.7.20200521s - see the following thread for more info: https://github.com/broadinstitute/gatk/issues/6708.

    You should continue to use funcotator_dataSources.v1.6.20190124 until GATK version 4.1.9.0 is released.

    Please let me know if you have any other questions or issues.

     

    Best,

    Samantha

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    sahuno

    Samantha-she-her Great! thanks for pointing this out!

    Sam

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    Samantha (she/her)

    Hi sahuno,

     

    Happy to help! If you need any further assistance, please let us know.

     

    Best,

    Samantha

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