Error loading tumor BAM in Mutect2 workflow

Post author
Tim Blewett

I am trying to run the GATK Mutect2 workflow, however, I am receiving the following error message:

Mutect2.tumor_reads_index - Expected single value for workflow input, but evaluated result set was empty
Mutect2.tumor_reads - Expected single value for workflow input, but evaluated result set was empty

 

Since there is no error messages regarding the normal BAM, I am confused why Terra is struggling to exclusively pull the tumor BAMs from the data tables. 

Comments

4 comments

  • Comment author
    Jason Cerrato

    Hi Tim,

    Thanks for writing in. I've migrated your inquiry to our General Discussion forum since it is not specifically about any of our featured workspaces.

    We'll be happy to assist you in finding an answer here! 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? The Share option is in the three-dots menu at the top-right.

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

    Please provide us with

    1. A link to your workspace
    2. The relevant submission ID
    3. The relevant workflow ID

    We’ll be happy to take a closer look as soon as we can.

    Kind regards,

    Jason

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  • Comment author
    Tim Blewett

    Hi Jason,

    Thanks for your help! Just shared the workspace and here is the relevant information:

    Let me know if you need anything else!

    Best,

    Tim

    0
  • Comment author
    Tim Blewett

    Hi Jason, 

    Just figured out my issue. I forgot to set the case_sample and control_sample attributes in the pairs table as references to the samples table. I am all set now.

    Best,

    Tim

    0
  • Comment author
    Jason Cerrato

    Hi Tim,

    Glad to hear! if we can assist with anything else, please let us know.

    Kind regards,

    Jason

    0

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