GenotypeGVCFs errors

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Nika Tsutskiridze

• May 14, 2021 14:47

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!

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  Jason Cerrato

  • May 14, 2021 20:06

  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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  Nika Tsutskiridze

  • May 14, 2021 21:53

  Shared! Please, have a look! Thanks

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  Jason Cerrato

  • May 17, 2021 13:12

  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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  Nika Tsutskiridze

  • May 17, 2021 13:39

  Hello Jason

  I have shared it via mail. Please check!

  Thanks!

  Nika

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  Jason Cerrato

  • May 17, 2021 14:10

  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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  Nika Tsutskiridze

  • May 17, 2021 15:28

  Ok, thanks! Looking forward to your response.

  Regards,

  Nika

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  Nika Tsutskiridze

  • May 17, 2021 17:51

  Hello Jason,

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

  Regards,

  Nika

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  Jason Cerrato

  • May 17, 2021 18:34

  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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  Nika Tsutskiridze

  • May 17, 2021 18:35

  Ok, thanks!

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  Jason Cerrato

  • May 17, 2021 19:08

  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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  Nika Tsutskiridze

  • May 17, 2021 19:16

  Ok, I will try it.

  Thanks!

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  Nika Tsutskiridze

  • May 18, 2021 10:22

  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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  Jason Cerrato

  • May 18, 2021 16:25

  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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  Nika Tsutskiridze

  • May 18, 2021 18:03

  Hello Jason,

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

  Regards,

  Nika

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  Nika Tsutskiridze

  • May 19, 2021 13:49

  Hello Jason,

  Is there any updates regarding my error?

  Thanks!

  Nika

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  Jason Cerrato

  • May 19, 2021 14:01

  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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  Nika Tsutskiridze

  • May 19, 2021 14:08

  Hello Jason,

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

  Thanks!

  Nika

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  Jason Cerrato

  • May 19, 2021 14:16

  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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  Nika Tsutskiridze

  • May 19, 2021 14:19

  Hello Jason,

  I think only this task(ImportGVCFs) need this flag

  Regards,

  Nika

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  Jason Cerrato

  • May 19, 2021 14:36

  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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  Nika Tsutskiridze

  • May 19, 2021 15:34

  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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  Jason Cerrato

  • May 19, 2021 15:41

  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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  Jason Cerrato

  • May 19, 2021 16:45

  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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  Jason Cerrato

  • May 19, 2021 17:22

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

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  Nika Tsutskiridze

  • May 19, 2021 17:42

  Hi Jason,

  Yes ,I am able to run this command

  Thanks,

  nika

   

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  Jason Cerrato

  • May 19, 2021 17:46

  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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  Nika Tsutskiridze

  • May 19, 2021 17:57

  Hi,

  NO i am not seeing this error.

  Kind Regards,

  Nika

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  Jason Cerrato

  • May 19, 2021 18:16

  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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  Nika Tsutskiridze

  • May 19, 2021 18:20

  Hi Jason,

  I am seeing the same error actually.

  Regards,

  Nika

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  Jason Cerrato

  • May 19, 2021 18:29

  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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