CGA WES Pipeline: fails to run, no informative error?

• 

  Jason Cerrato

  • May 11, 2020 14:26

  Hi Mia,

  Thank you for your inquiry. 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 (see the icon with the three dots 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 look and get back to you as soon as we can.

  Kind regards,

  Jason

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• 

  Mia Petljak

  • May 11, 2020 15:18

  Hi Jason,

   

  Thanks a million - I have shared the space now !

   

  workspace: 661-Clonal hematopoiesis

  workflow: CGA_WES_Characterization_Pipeline_v0.2_Jun2019

   

  Thanks !

  Mia

   

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• 

  Jason Cerrato

  • May 11, 2020 18:47

  Hi Mia,

  Would it be possible to be added to this authorization domain so that I can take a closer look?

  

  If not, please let me know and I'll try to find another way we can troubleshoot.

  Many thanks,

  Jason

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• 

  Mia Petljak

  • May 11, 2020 21:09

  Hi Jason,

  Thanks ! Am just checking with the relevant admins - would you need the same email to be added?

  Best,

  Mia

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  MPetlj

  • May 12, 2020 01:25

  Hi Jason,
  You should be added now -
  can you please check? Thanks!

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• 

  Jason Cerrato

  • May 12, 2020 13:03

  Hi Mia,

  I am indeed added! I'll take a look at this as soon as I can.

  Kind regards,

  Jason

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• 

  Jason Cerrato

  • May 12, 2020 14:58

  Hi Mia,

  Do you have access to any other workspaces you can share with me where this a submission with this workflow completed successfully?

  Kind regards,

  Jason

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• 

  MPetlj

  • May 12, 2020 15:11

  Hi Jason,

   

  I unfortunately do not! 

  Because it fails right at the beginning, the developers advised me (but don't have resources to provide further support) that this may be due to wrong workflow configuration or because I do not have access to one of the specified inputs. 

  I can access all of the inputs via google buckets, so don't think that is an issue...

  Thanks,

  Mia 

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• 

  Jason Cerrato

  • May 12, 2020 15:51

  Hi Mia,

  I think I may have found the error. Here is the error message you received:

  

   

  There are more, but they're all referring to not finding GatherWIGFiles_Task in the runtime_params map. This looks like it may be the point of the workflow this error is referencing:

  

   

  This cga_pipeline_config file points to this file from your Workspace Data.

  

  In that file, you'll notice there is no line for GatherWIGFiles_Task.diskGB_buffer (or any other GatherWIGFiles_Task lines for that matter), but this task does show up in the workflow and it tries to use the runtime_params file for the values.

  

   

  It seems to be the case that this json file is in error as it doesn't have a map for all of the tasks in the workflow. I'm curious to know if one or both of these options will resolve the issue for you:

  1. Add values for these optional parameters in the method configuration
     
  2. Add these lines to the json file just as lines exist for these variables for the other tasks in the workflow

   

  Let me know if either of these work for you!

  Kind regards,

  Jason

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• 

  MPetlj

  • May 12, 2020 16:36

  Hi Jason, 

  Very interesting and a good dig, thanks ! I was not paying attention to those as they are optional. I will try and let you know how it goes !

   

  Mia 

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• 

  MPetlj

  • Edited May 12, 2020 18:54

  Hi Jason,

  I see that the json file that is now in the workflow contains the lines you mention, so I assume you already did #2 and modified json to include these? 

  If that is correct, can you please see whether I correctly added specifications under the following, as the workflow still fails when I run it with inputs defined by the data table (Pair):

  caseName this.case_sample.sample_id

  ctrlName this.control_sample.sample_id

  normalBam this.control_sample.WES_GRCh37_bam

  normalBamIdx this.control_sample.WES_GRCh37_bai

  tumorBam this.case_sample.WES_GRCh37_bam

   

  tumorBamIdx this.case_sample.WES_GRCh37_bai

   

   

  If this is not the issue, perhaps it is worth trying your suggestion #1 and adding values to the missing variables, although these should be optional.

  Can you please tell me how to fill those in/is there a documentation on this? I am new to Terra/Cloud, not sure what I need to enter there.

  I will eventually want to run ~200 pairs.

   

  Thanks, 

  Mia 

   

  ERROR: 

  2020-05-12 18:31:02,268 INFO - MaterializeWorkflowDescriptorActor [UUID(0a281d6d)]: Parsing workflow as WDL draft-2
  2020-05-12 18:31:03,306 INFO - MaterializeWorkflowDescriptorActor [UUID(0a281d6d)]: Call-to-Backend assignments: CGA_Production_Analysis_Workflow.lego_plotter_task -> PAPIv2, CGA_Production_Analysis_Workflow.normalMM_Task -> PAPIv2, CGA_Production_Analysis_Workflow.VEP_Task -> PAPIv2, CGA_Production_Analysis_Workflow.Mutect1_Task -> PAPIv2, CGA_Production_Analysis_Workflow.Mutect2_Task -> PAPIv2, CGA_Production_Analysis_Workflow.GatherWIGFiles_Task -> PAPIv2, CGA_Production_Analysis_Workflow.merge_mafs_task -> PAPIv2, CGA_Production_Analysis_Workflow.oxoGOBF -> PAPIv2, CGA_Production_Analysis_Workflow.MutectFC_Task -> PAPIv2, CGA_Production_Analysis_Workflow.ffpeOBF -> PAPIv2, CGA_Production_Analysis_Workflow.Oncotate_Task -> PAPIv2, CGA_Production_Analysis_Workflow.CallSomaticMutations_Prepare_Task -> PAPIv2, CGA_Production_Analysis_Workflow.ContEST_Task -> PAPIv2, CGA_Production_Analysis_Workflow.absolute -> PAPIv2, CGA_Production_Analysis_Workflow.Strelka -> PAPIv2, CGA_Production_Analysis_Workflow.tumorMM_Task -> PAPIv2, CGA_Production_Analysis_Workflow.CrossCheckLaneFingerprints_Task -> PAPIv2, CGA_Production_Analysis_Workflow.mutation_validator -> PAPIv2, CGA_Production_Analysis_Workflow.gatk_acnv_only -> PAPIv2, CGA_Production_Analysis_Workflow.blat -> PAPIv2, CGA_Production_Analysis_Workflow.GatherAndDeTiN_Task -> PAPIv2, CGA_Production_Analysis_Workflow.MAFPonFilter -> PAPIv2, CGA_Production_Analysis_Workflow.CopyNumberReportQC_Task -> PAPIv2
  2020-05-12 18:31:51,890 INFO - $e [UUID(0a281d6d)]: Copying workflow logs from /cromwell-workflow-logs/workflow.0a281d6d-0250-4965-88c8-7031c35566ec.log to gs://fc-secure-a46c7502-d26e-4217-b1d4-7d80a20d7456/45180ae9-016d-4d29-a238-0a7070e43348/workflow.logs/workflow.0a281d6d-0250-4965-88c8-7031c35566ec.log

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• 

  Jason Cerrato

  • May 12, 2020 20:54

  Hi Mia,

  I have not made any modifications to the files. I also don't see that it's been changed—do you see the GatherWIGFiles_Task lines in the cga_pipeline_configs_optional_parameters.json?

  Because these are supposed to be optional, I think it might be best to try modifying this .json and adding the appropriate lines, or building a new .json with the same content but with the lines added. I noticed there are lines in the .json for Gather_Task.preemptible, Gather_Task.cpu, etc. but there's no Gather_Task in the WDL. I think these are supposed to be GatherWIGFiles_Task.

  I will email you a modified .json you can upload to a bucket and use instead of the one you are currently using. Let me know if you end up getting around your current issue after using it!

  Kind regards,

  Jason

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• 

  Liudmila Elagina

  • May 13, 2020 02:03

  Hello Mia,

   

  I think you were using configuration files for the first (v0.1) version of the CGA pipeline.

  For the second version (v0.2) of the CGA pipeline you can find in the open-access bucket:

  gs://getzlab-workflows-config_files/CGA_WES_Characterization/v0.2/cga_pipeline_config_optional_parameters.json

   

  Best,

  Luda

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• 

  Jason Cerrato

  • May 13, 2020 13:49

  Hi Mia,

  You may want to try the file Luda mentions above rather than trying to edit the current one. You can use the direct path to the file instead of the workspace.CGA_PIPELINE_CONFIG attribute.

  Kind regards,

  Jason

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• 

  Jason Cerrato

  • May 14, 2020 13:05

  Hi Mia,

  I will migrate this issue to a private ticket due to the amount of back-and-forth required. You will receive notification of this shortly.

  Kind regards,

  Jason

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