Job failing with exit 1 but displayed as succeeded in Terra

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12 comments

  • Sushma Chaluvadi

    Ilya,

    It would be easiest for us to determine what is causing this issue if we had access to your workspace! I believe you may have shared it with us previously but if not can you share the workspace and share the name/link? 

     

    Thanks!

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  • ilya_at_vivid

    I would rather not provide workspace names and links in this forum. Can I have a email address to send them to? I sent an email for a quota request and you could find my email there. I sent the email to:

    fc-quota-requests@googlegroups.com

     

    Thanks!

     

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  • Sushma Chaluvadi

    You can send an email to Terra-support@broadinstitute.zendesk.org and we will get an internal email!

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  • ilya_at_vivid

    Hi, I sent an email and did not receive a response. Now I got a message that my email bounced.

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  • Sushma Chaluvadi

    Hello Ilya -

    My apologies for the mistake in the email - a moment of copy paste gone wrong! Can you share your workspace with the user

    GROUP_FireCloud-Support@firecloud.org. We will be able to access the workspace once you add this user as a Writer atleast to your workspace. A link to the workspace is not necessary but a name of the workspace would be great. I can look into this asap.

     

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  • ilya_at_vivid

    I sent the information to the above email. Please let me know if it was received.

    Thanks,

    Ilya

     

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  • Sushma Chaluvadi

    Ilya -

    The email is a user email that the workspace needs to be shared with. Here is a screenshot:

     

    1. Click on the 3 dots to hit Share -

     

    2. Then add the user GROUP_FireCloud-Support@firecloud.org as Writer -

     

    This is the method by which you can *share* your workspace so that we can get access to look inside the logs and submissions that you ran.

    Thanks

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  • ilya_at_vivid

    Done. 

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  • Sushma Chaluvadi

    Ilya,

    Apologies for the back and forth but I am trying to look at this workspace and I see that it has an Authorization Domain, a group of which the above user is not member, and will need to be added to in order to enter the workspace. Can you add the GROUP_FireCloud-Support@firecloud.org also to the VividGenomics group? I believe you may have added my personal email before but the user above will allow our technical team to access as well.

     

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  • ilya_at_vivid

    Done

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  • Sushma Chaluvadi

    Ilya,

    We took a look at the stderr and the script and it looks like the Terra UI shows the submission as a Success because the final step `rm -rf geno-prefix pheno-file` results in the Exit code which is getting reported but the rest of the steps are failing. So since the last step is rendering as successful the UI shows it as a success.

    You can remove the rm step since any file not part of the `output` section is automatically removed when the task exits. By removing this step you should accurate visual of Failed in the UI. 

     

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  • ilya_at_vivid

    Makes sense. Good to know that the last exit code is the one read by Terra. Thanks you!

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