MirMachine Documentation

MirMachine is a command line workflow for detecting conserved miRNA families from genome FASTA files.

The MirMachine.py entry point prepares run metadata and launches a Snakemake workflow that generates:

• unfiltered GFF predictions

• filtered (high-confidence) GFF predictions

• FASTA sequences for predicted loci

• heatmap-ready summary tables

Contents:

• Installation
  • Recommended: Conda/Mamba (Bioconda)
  • From Source (Local Development)
  • Verify Installation
• Quick Start
  • Example 1: Standard Node-Based Run
  • Example 2: Restrict to a Single Node Only
  • Example 3: Single-Family Run
  • Discover Available Inputs
  • What Gets Created
• Core Concepts
  • Node
  • Family
  • Model
  • Search Scope Controls
  • Scoring and Confidence
  • Input Expectations
• Output
  • Main Output Layout
  • Interpretation
  • GFF Header Fields
  • Example GFF Row
  • FASTA files
  • Heatmap CSV
• CLI Options and Arguments
  • Command Modes
  • Run Examples
  • Arguments
  • Options
  • Notes
• Troubleshooting
  • Common Issues and Fixes
  • Invalid node name
  • Genome file error
  • Stalled Snakemake lock
  • Workflow cleanup
  • Low-confidence or sparse predictions
  • Family not found in single-family mode