Bio Annotation

Functional annotation and taxonomy inference from sequence homology.

Instructions

1. Run InterProScan for domain/family annotation.
2. Run eggnog-mapper for orthology-based annotation.
3. Run DIAMOND and resolve taxonomy with TaxonKit.

Quick Reference

Input Requirements

Prerequisites:

• Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Reference DB root: set BIO_DB_ROOT (default /media/shared-expansion/db/ on WSU).
• Input FASTA and reference DBs are readable.
  Inputs:
• proteins.faa (FASTA protein sequences).
• reference_db/ (eggNOG, InterPro, DIAMOND databases + taxdump).

Output

• results/bio-annotation/annotations.parquet
• results/bio-annotation/taxonomy.parquet
• results/bio-annotation/annotation_report.md
• results/bio-annotation/logs/

Quality Gates

• Annotation hit rate and taxonomy rank coverage meet project thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• Verify proteins.faa is non-empty and amino acid encoded.
• Verify required reference DBs exist under the reference root.

Examples

Example 1: Expected input layout

proteins.faa (FASTA protein sequences).
reference_db/ (eggNOG, InterPro, DIAMOND databases + taxdump).

Troubleshooting

Issue: Missing inputs or reference databases
Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates
Solution: Review reports, adjust parameters, and re-run the affected step.