{
  "status": "ready_for_full_genome_pilot",
  "simulator": {
    "name": "ART-modern",
    "version": "1.3.2",
    "source_commit": "133ec34368f7bd0083e1f2dfe3b0f56fbe08b465",
    "upstream_unmodified": true,
    "archive_url": "https://github.com/YU-Zhejian/art_modern/releases/download/1.3.2/build_rel_with_dbg_alpine-x86_64.tar.gz",
    "archive_sha256": "1d443209fbf773424e6768b5f050564b56149ba83c354e873b48cf5d55618f96",
    "binary": "bin-1.3.2/art_modern",
    "binary_sha256": "24ba37808374e4924bcd865c0947d042cc30540af1ed6d9f83de5ef437c2e193"
  },
  "profile": {
    "study": "PRJEB90663",
    "run": "ERR15382247",
    "platform": "Illumina NovaSeq X Plus",
    "primary_paper": "https://doi.org/10.1093/nargab/lqag053",
    "pairs": 100000,
    "source_read_length": 151,
    "simulated_read_length": 150,
    "quality_bins": [
      2,
      12,
      24,
      40
    ],
    "files": {
      "R1": {
        "path": "NovaSeqX_ERR15382247_R1.txt",
        "sha256": "3a970b8a79858fe64004572efb43b323abc567cc9d3145ce20588395234bc313"
      },
      "R2": {
        "path": "NovaSeqX_ERR15382247_R2.txt",
        "sha256": "ac9c96a4b2745ec37e6d72295f89c33766dd08460092d6480d82c0cf4e68f15f"
      }
    },
    "receipt_sha256": "6a5f875166daa45a527c0f98b083a84cd52b7dcd01642710f2cc26160180bb7f"
  },
  "interface": {
    "wrapper": "simulate_haplotype.py",
    "wrapper_sha256": "0a31cd36f3f4db473e0ce8569cc50ad236d62abc1f4852f71207a997901468ab",
    "argv": [
      "python3",
      "simulate_haplotype.py",
      "--input",
      "HAPLOTYPE.fa",
      "--output-prefix",
      "OUT/hap1",
      "--name-prefix",
      "DONOR_hap1",
      "--seed",
      "SEED",
      "--threads",
      "8",
      "--coverage",
      "15"
    ],
    "output_mates": [
      "OUT/hap1_R1.fastq.gz",
      "OUT/hap1_R2.fastq.gz"
    ],
    "completion": "OUT/hap1.COMPLETE.json",
    "seed_contract": [
      1,
      2147483647
    ],
    "native_seed_type": "uint64_t; conservative contract restricts to signed32 positive",
    "overwrites": false,
    "max_pending_mates": 1000000
  },
  "model": {
    "coverage_per_haplotype": 15,
    "coverage_diploid_total": 30,
    "paired_end": true,
    "read_length": 150,
    "fragment_mean": 350,
    "fragment_sd": 50,
    "insertion_rate": 0,
    "deletion_rate": 0,
    "indels": "zero; explicit assumption, not empirically calibrated",
    "substitutions": "ART standard independent Phred-derived perbase probability10^(-Q/10), alternate bases sampled by ART",
    "quality": "independent empirical mate/cycle marginals",
    "max_n": 0,
    "contig_boundary": "No fragment crosses FASTA records. Contigs below250bp skipped; fragment length rejected untilfits record. Ns in sequenced read ends rejected/retried; internal insert Ns can remain unsequenced.",
    "limitations": [
      "Prefix/tile-limited single-run sample, not representative of all NovaSeqX instruments/runs.",
      "No empirical context/homopolymer/PCR/GC coverage bias or crosscycle error correlations.",
      "Large-N records can underproduce when simulator failure budget reached; fullWGS QC must inspect achieved coverage, contig counts and stderr."
    ]
  },
  "validation": {
    "fixture_only": true,
    "full_genome_pilot_required": true,
    "toy_validation_sha256": "fc7d7d1d437d7107c84f2697c376b6980da0924d4099e72dadcc2faedc3f6107",
    "wrapper_fixture": {
      "pairs": 10000,
      "maximum_pending_mates": 1,
      "bases": 3000000
    }
  }
}