RADinitio version 1.2.3
radinitio.simulate started on 2025-10-21 15:55:05.

Dependency versions:
    msprime:                 1.3.4
    decoratio:               1.0.5
    numpy:                   1.23.5
    scipy:                   1.10.0

Target sequences not specified. Simulating over all sequences in the reference genome.
    Keeping sequences larger than 5,000 bp.

msprime demographic model options:
    Mutation rate:           7e-08
    Number of populations:   2
    Pop 1 Ne:                5000.0
    Pop 1 sample size:       10
    Pop 2 Ne:                5000.0
    Pop 2 sample size:       10
    Migration matrix:
             [0, 0.001]
             [0.001, 0]

Mutation options:
    substution model:        equal
    indel probability:       0.01
    insert/deletion ratio:   1

RAD Library Options:
    library type:            ddRAD
    restriction enzyme 1:    MseI (T/TAA)
    restriction enzyme 2:    EcoRI (G/AATTC)
    insert size mean:        350 bp
    insert size min:         280 bp
    insert size max:         420 bp
    read length:             150 bp
    sequencing coverage:     20 x
    read1 barcode length:    5 bp
    read2 barcode length:    0 bp
    5' sequencing error:     0.001
    3' sequencing error:     0.01
    base locus length:       1,000 bp
    min locus distance:      1,000 bp
    max proportion Ns:       0.1

PCR model options:
    PCR amplification model: None (No PCR)
    PCR cycles:              None
    PCR duplicate rate:      0.00%

Loading the genome...
    Read 1,663 sequences from the input FASTA.
    Loaded 1,663 chromosome/scaffold sequences.

Simulating chromosomes with msprime...
    CM075516.2...
    JBBGZY020000001.1...
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