Call input and runtime attributes evaluation failed for PairedFastQsToUnmappedBAM

[Ananya-swi]

Hi,

I am trying to run the Example Workflow: Convert FASTQ files to uBAM file using Cromwell On Azure.

I used the publicly available input file URLs and uploaded into the "inputs" container in Cromwell on Azure storage account "demo0fd990508f1745" associated with the host VM.
While running the example workflow, I got the below error message:

{
  "WorkflowUrl": "https://demo0fd990508f1745.blob.core.windows.net/inputs/paired-fastq-to-unmapped-bam.wdl",
  "WorkflowInputsUrl": "https://demo0fd990508f1745.blob.core.windows.net/inputs/paired-fastq-to-unmapped-bam.inputs.json",
  "WorkflowInputsUrls": null,
  "WorkflowOptionsUrl": null,
  "WorkflowDependenciesUrl": null,
  "WorkflowFailureInfo": {
    "WorkflowFailureReason": "CromwellFailed",
    "CromwellFailureLogs": [
      {
        "Message": "Workflow failed",
        "CausedBy": [
          {
            "Message": "Call input and runtime attributes evaluation failed for PairedFastQsToUnmappedBAM",
            "CausedBy": [
              {
                "Message": "Failed to evaluate input 'disk_space_gb' (reason 1 of 1): [Attempted 1 time(s)] - NoSuchFileException: /demo0fd990508f1745/inputs/seq-format-conversion/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq",
                "CausedBy": []
              }
            ]
          }
        ]
      }
    ]
  }
}

The Used inputs.json file is the below one.

{
  "ConvertPairedFastQsToUnmappedBamWf.readgroup_name": "NA12878_A",
  "ConvertPairedFastQsToUnmappedBamWf.sample_name": "NA12878",
  "ConvertPairedFastQsToUnmappedBamWf.fastq_1": "/demo0fd990508f1745/inputs/seq-format-conversion/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq",
  "ConvertPairedFastQsToUnmappedBamWf.fastq_2": "/demo0fd990508f1745/inputs/seq-format-conversion/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_2.fastq", 
  "ConvertPairedFastQsToUnmappedBamWf.library_name": "Solexa-NA12878",
  "ConvertPairedFastQsToUnmappedBamWf.platform_unit": "H06HDADXX130110.2.ATCACGAT",
  "ConvertPairedFastQsToUnmappedBamWf.run_date": "2016-09-01T02:00:00+0200",
  "ConvertPairedFastQsToUnmappedBamWf.platform_name": "illumina",
  "ConvertPairedFastQsToUnmappedBamWf.sequencing_center": "BI",
  "ConvertPairedFastQsToUnmappedBamWf.make_fofn": true  
}

The same example wdl file is used for processing (https://github.com/microsoft/seq-format-conversion-azure/blob/main-azure/paired-fastq-to-unmapped-bam.wdl) along with the trigger json file.

Can you help me understand the issue (the input fastq files are available inside the folder)?