End-to-end GWAS Imputed Data QC

Ilakya Selvarajan

Hi!

I'm running the end to end GWAS tutroial and face some errors in the imputed data QC step: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/end-to-end-target-discovery-with-gwas-and-phewas#imputed-data-qc

Following the CLI/UI instructions, I applied the header correction suggested for GEL. However, the workflow fails at the scatter (i in range(length(geno_bgen_files))) step with this error: A job in the job tree named "bgens_qc_frag_stage-0 22" running function "main" of "bgens_qc_frag_stage-0" failed because of AppInternalError: Error evaluating input geno_sample_file value ExprAt(ExprIdentifier(geno_sample_files,T_Array(T_File,true)),ExprIdentifier(i,T_Int),T_File) to call bgen_qc

 

Alternatively, I ran generate_inputs.ipynb, which successfully generates bgens_qc_input.json in RAP. 

I now want to compile the workflow from my Mac using:

 java -jar <path_to_downloaded_dxCompiler>dxCompiler-2.XX.X.jar compile research_project/bgens_qc/bgens_qc.wdl -project project-XXX -inputs research_project/bgens_qc/bgens_qc_input.json -archive -folder '<path_to_folder_on_UKB_RAP>'

This command works well when I compile bgens_qc.wdl (without -inputs). But when I add the location of bgens_qc_input.json (which is in RAP), it fails to recognise the file. 

Can you please help me?

 

 

Comments

2 comments

Date Votes
  • Comment author
    Eric Kernfeld

    Can you share the value you are using for <path_to_folder_on_UKB_RAP>? For mine, I succeeded with /olink_data_53k/GWAS, where olink_data_53k is a subfolder of my main project folder (shown in screenshot).  

    1
  • Comment author
    Ilakya Selvarajan

    Hi Eric,

    Thanks for your reply! I managed to run the scatter loop successfully. The error occured because I had selected both the .bgen and .bgen.bgi files as input.

    1

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