Bio Annotation

Functional annotation and taxonomy inference from sequence homology.

Instructions

1. Read docs/README.md and the relevant tool guides before running anything.
2. For InterProScan, read docs/interproscan-usage.md and validate the exact CLI with --help or --version.
3. Run InterProScan for domain/family annotation.
4. Run eggnog-mapper for orthology-based annotation.
5. Run DIAMOND and resolve taxonomy with TaxonKit.

Quick Reference

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See docs/README.md.

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 proteins.faa does not contain * stop symbols before InterProScan, or strip them deliberately.
• Verify InterProScan output options are valid: use -b or -d, never both together.
• Verify packaged InterProScan installs have been initialized with python3 setup.py -f interproscan.properties when required.
• Verify required InterProScan helper binaries are resolvable, especially ps_scan.pl, pfscan, and pfsearch.
• Run a small login-node smoke test on 1-2 proteins before submitting a large cluster job.
• 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: InterProScan fails immediately with CLI or runtime setup errors Solution: Check docs/interproscan-usage.md for mutually exclusive output flags, * stripping, one-time setup.py initialization, and ProSite PATH requirements.

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