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
Hi Nika,
It looks like the enabling of requester pays is causing an unexpected error when running workflows in the workspace. Would you be okay with us reverting the requester pays setting for the time being while the engineers investigate so you can run your workflows?
And out of curiosity, what is your end goal for having the buck enabled with requester pays?
Kind regards,
Jason
Hello Json,
I have run this workflow on my another workspace and everything is running successfully. We currently have an error on CrossCheckFingerprintSolo it needs this flag --gcs-for-requester-pays. It is totally my fault i should have know about this. Please let me know if we can add this flag. Thank you again and again you are very helpful.
Many Thanks!
Best regards,
Nika
Hi Nika,
Thanks for letting me know. I'll prepare a new version of that workflow shortly.
I've learned an important piece of information regarding requester pays buckets: workspaces with RP buckets will not be able to run workflows. As such, would you like RP disabled for your workspace joint-genotyping, or would you like to keep RP enabled? What is your end goal for having RP enabled on this workspace?
Kind regards,
Jason
Hi Nika,
Here is a new version that includes the option to provide the project to bill for the CrossCheckFingerprint task.
https://portal.firecloud.org/#methods/jcerrato/JointGenotyping_v1.5.1_RPbuckets/3
You can provide for the Solo and/or Scattered version of the task. I assume this will depend on your run!
Kind regards,
Jason
Hi Jason!
I have imported this workflow but it is giving me this error.Please have a look at it.
kind Regards,
Nika
Hi Nika,
Aha, it looks like the CrosscheckFingerprints command doesn't have this flag.
Can you share the other workspace you're running these workflows in with GROUP_FireCloud-Support@firecloud.org and provide me a link so I can take a look at your recent runs?
Can you also confirm whether you would like us to disable requester pays for your joint-genotyping workspace?
Kind regards,
Jason
Hi Jason,
Yes, I want to disable requester pays for joint-genotyping. Actually this workspace isn't mine and it will take a lot of time before i get permission to share this. If you will disable Joint-genotyping requester pays option. I can run the workflow there. Configuration of workflows are the same and it will gives us same results.
Best regards,
Nika
Hi Nika,
Requester pays has been turned off for the joint-genotyping workspace. You should be able to run workflows in that workspace again. Let us know if you run into any problems!
Kind regards,
Jason
Hello Jason!
Thank you very much! I have started running workflow there. You can monitor it now. Thanks again. And also I have one question can you add allow_old_rms_mapping_quality_annotation flag to this https://portal.firecloud.org/?return=terra#methods/gatk/joint-discovery-gatk4/14 version of workflow.
Many Thanks!
Best Regards,
Nika
Hi Nika,
Just curious: Is there a particular reason you need the older version of JointGenotyping modified, or why modifying the version I've set up wouldn't work for your needs?
By the way, this WDL is fairly easy to make a new version of because it doesn't rely on any subworkflows. As such, you can Clone this WDL and modify it to your heart's content, then export it to your workspace for use.
Kind regards,
Jason
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