Call input and runtime attributes evaluation failed for PairedFastQsToUnmappedBAM
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)?
-
Hi Ananya,
This document should explain how to set up the inputs (and how the fastq files should be accessible).
Hope that helps.
- George
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