Download Databases

Install Databases (Kneaddata, MetaPhlAn, HUMAnN)

Essential first step to download and install required reference databases for all MetaGEAR workflows.

Description

The download_databases workflow downloads and installs the required databases for MetaGEAR workflows. This includes:

  • MetaPhlan database - For species profiling
  • HUMAnN database - For functional profiling
  • GTDBTk database - For Taxonomic annotation

Parameters

This workflow has no specific parameters. It only accepts global parameters.

Global Parameters

Parameter Required Default Description
--outdir No results Output directory where databases will be installed
--help No - Display help information
--debug No false Enable debug mode
--config No - Custom configuration file

Syntax 

metagear download_databases [GLOBAL_OPTIONS]

Examples

Basic Usage 

# Download databases to default location (./results)
metagear download_databases

# Download databases to custom directory
metagear download_databases --outdir /path/to/databases

# Enable debug mode for troubleshooting
metagear download_databases --debug

Preview Mode 

# Generate script without executing
metagear download_databases --preview

This will create a metagear_download_databases.sh script that can be reviewed and executed manually.

Output

The workflow downloads and installs databases to the configured locations:

outdir/
├── kneaddata/                   # Kneaddata contamination removal databases
│   └── human_genome/            # Human genome reference database
│       ├── human_genome.1.bt2   # Bowtie2 index files
│       ├── human_genome.2.bt2
│       ├── human_genome.3.bt2
│       ├── human_genome.4.bt2
│       ├── human_genome.rev.1.bt2
│       └── human_genome.rev.2.bt2
├── metaphlan/                   # MetaPhlAn taxonomic profiling databases
│   └── metaphlan_db_latest/     # MetaPhlAn database directory
│       ├── mpa_latest           # Database version marker
│       ├── *.bt2                # Bowtie2 index files for species markers
│       ├── *.pkl                # Pickle files with taxonomic data
│       ├── *.fna.bz2            # Compressed marker gene sequences
│       └── *.md5                # Checksum files
├── humann/                      # HUMAnN functional profiling databases
│   ├── chocophlan/              # ChocoPhlAn species-specific pangenomes
│   │   └── full/                # Complete ChocoPhlAn database
│   └── uniref/                  # UniRef protein families database
│       └── uniref90_diamond/    # UniRef90 Diamond-formatted database
└── pipeline_info/               # Pipeline execution metadata
    ├── execution_report.html    # Nextflow execution report
    ├── execution_timeline.html  # Processing timeline
    └── execution_trace.txt      # Resource usage tracking

Key Output Files

Contamination removal database:

  • kneaddata/human_genome/ - Human genome reference for host sequence removal

Taxonomic profiling database:

  • metaphlan/metaphlan_db_latest/ - Complete MetaPhlAn database with marker genes and taxonomic classifications

Functional profiling databases:

  • humann/chocophlan/full/ - Species-specific pangenome database for functional annotation
  • humann/uniref/uniref90_diamond/ - Protein family database for functional classification

Notes

  • Database sizes: Downloads can be 10-50GB+ total and may take hours to complete
  • Network requirements: Stable high-speed internet connection recommended
  • Disk space: Ensure 100GB+ free space before starting
  • One-time setup: This workflow only needs to be run once per MetaGEAR installation
  • Database updates: Databases are periodically updated; re-run to get latest versions
  • Storage location: Databases are stored according to configuration file settings

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