GenotypeGVCFs errors

Hello everyone!

I am trying to run joint-discovery workflow, but I am getting this error : A USER ERROR has occurred: use-new-qual-calculator is not a recognized option, when I am using broadinstitute/gatk:4.1.5.0 and this :A USER ERROR has occurred: Bad input: Presence of '-RAW_MQ' annotation is detected. This GATK version expects key RAW_MQandDP with a tuple of sum of squared MQ values and total reads over variant genotypes as the value. This could indicate that the provided input was produced with an older version of GATK. Use the argument '--allow-old-rms-mapping-quality-annotation-data' to override and attempt the deprecated MQ calculation. There may be differences in how newer GATK versions calculate DP and MQ that may result in worse MQ results, when I am trying to use the latest gatk version. Can anyone help me?

Thank you in advance!

Comments

40 comments

  • Comment author
    Jason Cerrato

    Hi Nika,

    Thank you 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? 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.

    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!

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Shared! Please, have a look! Thanks

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  • Comment author
    Jason Cerrato

    Hi Nika Tsutskiridze,

    We'll be happy to! Can you please share a link to the workspace or provide its name, as well as the submission ID to investigate?

    Many thanks,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hello Jason

    I have shared it via mail. Please check!

    Thanks!

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Got it - thank you! We are experiencing a higher-than-usual volume of support requests, so it may take a little longer for us to get back to you but we are working as quickly as we can!

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Ok, thanks! Looking forward to your response.

    Regards,

    Nika

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    Is there any progress? I am a little bit in hurry.

    Regards,

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Apologies for the wait - as mentioned we are experiencing a high volume of requests. I will take a quick look now to see if I can discern why you are experiencing this issue as there is some urgency around this request.

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Ok, thanks!

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Even though you are using the latest GATK docker version, I see you are not using the latest version of the workflow. You can find the latest version in the featured workspace GATK4-Germline-Preprocessing-VariantCalling-JointCalling.

    This is the latest version of the workflow: https://dockstore.org/workflows/github.com/broadinstitute/warp/JointGenotyping:JointGenotyping_v1.5.1?tab=files

    I would recommend trying this version to see if it resolves your issue!

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Ok, I will try it.

    Thanks!

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    I have imported latest version of the workflow in my workspace and configure it with every parameters. But unfortunately at the ImportGVCFs stage I am getting this error. Do you have any suggestions how to fix it.

    Thanks in advance!

    Regards, Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Based on the message in that error, it looks like you are trying to access files from a requester pays bucket but have not provided a project to bill for retrieval of the data. This command requires the addition of the --gcs-for-requester-pays flag with the GenomicsDBImport command when using data from a requester pays bucket. It looks like the current version of the workflow doesn't have this flag by default, so I'll work on getting you an alternate version that includes the flag. I'll follow up here once it's available.

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    Thank you for response! I will wait for your reply.

    Regards,

    Nika

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    Is there any updates regarding my error?

    Thanks!

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Apologies for the wait. The WARP Github repository is currently restricted so I am not able to make a new branch with the change needed. I'm currently looking to get permission from the team to make a branch, or see if they will be able to implement this change for us.

    If this is very urgent, I can make a version of the workflow on the Broad Methods Repository you can use. You'll have to import it as a new method, though. Let me know if you need this ASAP.

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    This task is very urgent. It would be great if you make this method.

    Thanks!

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Understood, I'll get that method to you as quickly as I am able. Can you confirm which tasks will be utilizing data from a requester pays workspace? I see the ImportGVCFs task failed for not having this flag, but I'd like to know in advance, if possible, whether any other tasks can expect to use RP bucket data.

    Many thanks,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hello Jason,

    I think only this task(ImportGVCFs) need this flag

    Regards,

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Here is a new version of the workflow that gives you the option of providing a project to bill for requester pays data in the ImportGVCFs task.

    https://portal.firecloud.org/#methods/jcerrato/JointGenotyping_v1.5.1_RPbuckets/2 

    Let me know if this works for your needs. 

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hello Json,

    Thanks for making it. Can you tell me exactly with which parameter should I populate this variable?

    Thanks

    Nika

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  • Comment author
    Jason Cerrato

    Hey Nika,

    You'll simply need to provide the Google project you want to bill for use of this data. This can be the Terra billing project for the workspace you're running this workflow in.

    Kind regards,

    Jason

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  • Comment author
    Jason Cerrato

    Hi Nika,

    I see you requested that requester pays be enabled on this bucket, which was enabled by one of our engineering teams recently. Perhaps there's a link there.

    Can you confirm whether you are able to successfully run this command in a Terminal?

    gsutil -u joint-genotyping ls gs://fc-4ce41a17-f9de-40c4-b42a-a0bd3d45ef08

    Many thanks,

    Jason

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  • Comment author
    Jason Cerrato

    Please also let us know if you are seeing any error messages associated with the bucket when visiting your workspace.

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  • Comment author
    Nika Tsutskiridze

    Hi Jason,

    Yes ,I am able to run this command

    Thanks,

    nika

     

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Thanks for confirming. Do you see this error message when visiting your workspace, or does all look normal on your end?

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hi,

    NO i am not seeing this error.

    Kind Regards,

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Thanks for confirming. Can you try re-running your workflow and letting us know if you see the same error occur?

    Kind regards,

    Jason

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  • Comment author
    Nika Tsutskiridze

    Hi Jason,

    I am seeing the same error actually.

    Regards,

    Nika

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  • Comment author
    Jason Cerrato

    Hi Nika,

    Thanks for confirming so quickly. One of our engineers will take a closer look right away.

    Kind regards,

    Jason

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