OMAmer HOG¶
Overview¶
The OMAMER_HOG process performs orthology inference using OMAmer (Orthologous MAtrix MER), searching protein sequences against a hierarchical orthologous groups (HOG) database to assign proteins to orthologs.
Process Details¶
- Label:
omamer - Tag: Uses genome assembly accession (
meta.gca) - Store Directory:
${params.cacheDir}/${meta.gca}/omamer/ - Max Forks: 15 (limits parallel execution)
Inputs¶
| Name | Type | Description |
|---|---|---|
| meta | val | Metadata map containing genome assembly info |
| translation_file | path | FASTA file containing protein translations to analyze |
Required Metadata Fields¶
gca: Genome assembly accession
Outputs¶
| Channel | Type | Description |
|---|---|---|
| omamer_hog_output | tuple | Metadata and OMAmer output file (proteins.omamer) |
| versions_file | path | versions.yml file tracking OMAmer version |
Parameters¶
Required¶
params.cacheDir: Cache directory for storing OMAmer resultsparams.omamer_database: Path to OMAmer HOG database
Optional¶
params.files_latency: Delay after script execution (default handled by afterScript)
Script Details¶
The process:
1. Executes omamer search against the specified HOG database
2. Analyzes input protein sequences from the translation file
3. Assigns proteins to hierarchical orthologous groups
4. Outputs results to proteins.omamer file
5. Captures OMAmer version from pip package information
Dependencies¶
- OMAmer (Python package)
- OMAmer HOG database
- Python 3 with pip
Storage Strategy¶
Uses storeDir directive to cache results permanently by genome assembly accession, avoiding redundant orthology searches for the same proteins.
Output Format¶
The proteins.omamer file contains orthology assignments in OMAmer's native format, which can be consumed by downstream tools like OMark for quality assessment.
Notes¶
- Results are cached permanently to avoid re-running expensive orthology searches
- Maximum of 15 concurrent processes to manage computational resources
- The process includes a configurable sleep delay after completion to handle file system latency
- OMAmer version is extracted from pip package metadata