{
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  "r1_filename": "Vibrio-Al_L001_R1_001.fastq",
  "r2_filename": "Vibrio-Al_L001_R2_001.fastq",
  "pipeline_status": "COMPLETED",
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  "raw_qc_status": "COMPLETED",
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  "trimmed_qc_status": "COMPLETED",
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  "multiqc_status": "COMPLETED",
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  "quast_status": "COMPLETED",
  "annotation_status": "COMPLETED",
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  "pipeline_start_time": "2026-09-14T13:41:12.598599722Z",
  "pipeline_completion_time": "2026-09-14T13:41:13.444438Z",
  "pipeline_version": "1.0.0",
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    "r2_filename": "Vibrio-Al_L001_R2_001.fastq",
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    "stage_status": "COMPLETED",
    "overall_qc_result": "FAIL",
    "files": [
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        "archive": "Vibrio-Al_L001_R1_001_fastqc.zip",
        "modules": {
          "Basic Statistics": "PASS",
          "Per base sequence quality": "FAIL",
          "Per tile sequence quality": "PASS",
          "Per sequence quality scores": "WARN",
          "Per base sequence content": "FAIL",
          "Per sequence GC content": "PASS",
          "Per base N content": "PASS",
          "Sequence Length Distribution": "WARN",
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          "Adapter Content": "WARN"
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          "Encoding": "Sanger / Illumina 1.9",
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          "%GC": "46"
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        "filename": "Vibrio-Al_L001_R1_001.fastq",
        "overall_qc_result": "FAIL"
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      {
        "archive": "Vibrio-Al_L001_R2_001_fastqc.zip",
        "modules": {
          "Basic Statistics": "PASS",
          "Per base sequence quality": "FAIL",
          "Per tile sequence quality": "PASS",
          "Per sequence quality scores": "WARN",
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          "Filename": "Vibrio-Al_L001_R2_001.fastq",
          "File type": "Conventional base calls",
          "Encoding": "Sanger / Illumina 1.9",
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          "%GC": "46"
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    "parameters": "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50"
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    "overall_qc_result": "FAIL",
    "files": [
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          "Per base sequence quality": "PASS",
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          "%GC": "44"
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        "modules": {
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        "overall_qc_result": "FAIL"
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    "report": "multiqc_report.html"
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    "reason": null,
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      "Vibrio-Al.gbff",
      "Vibrio-Al.gff3",
      "Vibrio-Al.hypotheticals.faa",
      "Vibrio-Al.hypotheticals.tsv",
      "Vibrio-Al.inference.tsv",
      "Vibrio-Al.json",
      "Vibrio-Al.log",
      "Vibrio-Al.png",
      "Vibrio-Al.svg",
      "Vibrio-Al.tsv",
      "Vibrio-Al.txt"
    ]
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    "Trimmomatic": "0.41",
    "SPAdes": "4.3.0",
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    "Bakta": "bakta 1.11.4",
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    "Nextflow": "26.04.6",
    "WGS pipeline": "1.0.0"
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}
