Issues with H1N1 and H3N2 Virus Analysis using Augur Workflow

I am currently analyzing data on H1N1 and H3N2 viruses using the 'augur phb flu' workflow. However, I've encountered some issues. Firstly, although the Augur run for H1N1 was successful, I'm unable to locate the JSON file necessary for uploading in Auspice. Additionally, upon examining the Newick tree file with Mega, I noticed some missing information in the tree. As for H3N2, the Augur prep was successful, but I'm encountering an error during the Augur run. I would appreciate any assistance in resolving this issue. Thank you in advance

Comments

9 comments

  • Comment author
    Pamela Bretscher

    Hi Ana,

    Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Toggle the "Share with support" button to "Yes"
    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,

    Pamela

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  • Comment author
    Ana Shubitidze
    • Edited

    Hello, The main issue concerns the JSON file and the missing information on the tree - 
    The link to the workspace - https://app.terra.bio/#workspaces/aphl-personal/APHL_Lugar_Center_ToT/data
    The submission ID - 1e5b985f-8625-4d97-acac-97a6e42f3544
    The relevant workflow ID - aphl-personal/Augur_PHB_flu_Y31hjMUcS4Y.

     As for H3N2, the Augur prep was successful, but I'm encountering an error during the Augur run.
    The link to the workspace - https://app.terra.bio/#workspaces/aphl-personal/APHL_Lugar_Center_ToT/data
    The submission ID - 6e6f1a21-3149-48c8-969b-089ad65b907b
    The relevant workflow ID - aphl-personal/Augur_PHB_flu_Y31hjMUcS4Y.

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  • Comment author
    Pamela Bretscher

    Hi Ana,

    Thanks for providing this information. The submission IDs you provided actually look like the IDs for the Google buckets for the workspaces. Can you provide the submission IDs for the workflow submissions you are having issues with? You can find these in your job history for the workspace.

    Kind regards,

    Pamela

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  • Comment author
    Ana Shubitidze

    Oh sorry, I updated the previous comment. Please take a look. Thank you

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  • Comment author
    Ana Shubitidze

    Thank you so much for your assistance. I appreciate your help. However, due to the time difference, our conversation is taking longer than expected. Would it be possible for us to schedule a call? 

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  • Comment author
    Pamela Bretscher

    Hi Ana,

    I have been working to investigate your issues, I just haven't yet been able to determine why these issues are occurring. I will let you know as soon as I have any further information for you.

    Kind regard,

    Pamela

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  • Comment author
    Anthony DiCi

    Hi Ana,

    My name is Anthony, and I will be assisting you with this issue going forward. I would be more than happy to set up a call with you to troubleshoot together. Do you have availability tomorrow? I'm not sure of the extent of the time difference, so please let me know what times you are free.

    I look forward to your reply!

    Best,

    Anthony

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  • Comment author
    Ana Shubitidze

    Hi,
    Thank you for your response. Anytime works for me, but please remember that I'm in the (GMT+4) time zone.

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  • Comment author
    Anthony DiCi

    Hi Ana,

    I've sent you an email to continue our scheduling. 

    I look forward to your reply!

    Best,

    Anthony

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