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Beginner's question: Why can't I start the analysis run on Terra?

drburndrburn SeattleMember
Hello.

I am new in genomic analysis and GATK. I am trying to start Haplotypecaller workflow on Terra. I have uploaded aligned genomic reads (bam file and bam index) and used appropriate genome assembly provided by the system (b37). However, 'Run Analysis' button is still gray and Outputs tab in the workflow is marked with exclamation sign (missing parameters). I can not change anything in the Outputs tab. There is only a text "Output files will be saved to
Files / submission unique ID / haplotypecaller-gvcf-gatk4 / workflow unique ID" and I can not do anything in that tab. I attached a screenshot, what the page looks like.

I have installed gatk on my personal laptop too and I successfully ran the analysis on it with the same data. However, I want to be able to use Terra cloud service for further needs so I really would like to repeat this training analysis on Terra. Most likely I missed some obvious step, but I ran out of ideas what it may and hope that more experiences users can help. Thank you for any advice.

Best Answer

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited July 25

    Hi @drburn

    I am going to pass this question to the Terra team and someone from that team should be able to help you with this.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hello @drburn, If you are able to, can you share the workspace with [email protected] as a Writer (you can remove this permission once we have resolved the issue)? You may need to share any Workflows that are not already publicly readable independent of the Workspace - this can be done through the FireCloud Methods Repository which you can access with this link https://portal.firecloud.org/?return=terra#methods. Sharing the Workspace will allow us to look directly into the logs and troubleshoot more efficiently.

  • drburndrburn SeattleMember
    @SChaluvadi,

    I just shared the workspace. Thank you for looking into that.
  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited August 1

    @drburn - I am unable to find the workspace, can you list the name of the workspace and also double check that it was shared correctly?

    Have you have uploaded your bam/bai files to the workspace's google bucket and then updated the Data Model?

    You will need to follow the general steps below to set up the Data Model and launch the analysis:
    Uploading to a workspace Google bucket

    Linking data in a Google bucket to your workspace

    Configure a workflow to process your data

    If you do not want to update your Workspace's data model:
    1. Click on Inputs.
    2. In the Attributes columns, you will need to add the path to the files that are uploaded to the Google bucket. It should look something like "gs://fc-*****/path/to/input.bam" (quotes included).
    3. Once all the paths to the input files are put in, you will need to press Save and the Run Analysis button should highlight.

    If you share the name of your Workspace, I am more than happy to take a closer look.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @drburn If you would like to attend our training sessions to onboard new users to Terra, please write to our Terra support desk [email protected] and we can set you up to attend classes remotely via Google Hangouts.

  • drburndrburn SeattleMember
    @SChaluvadi ,

    1) I would love to attend training sessions remotely. Thank you.

    2) I shared the workspace with [email protected] as you suggested. In my Terra account, the workspace is named Variants.

    3) I did all the steps you mentioned: uploaded bam files, linked them to workflow, linked genome reference files available at Terra to the workflow.

    Thank you for looking into the issues.
    Nikolay.
  • drburndrburn SeattleMember
    @SChaluvadi

    Thank you for looking into that. I will try this solution!
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