Bio Annotation
Functional annotation and taxonomy inference from sequence homology.
Instructions
- Read
docs/README.mdand the relevant tool guides before running anything. - For InterProScan, read
docs/interproscan-usage.mdand validate the exact CLI with--helpor--version. - Run InterProScan for domain/family annotation.
- Run eggnog-mapper for orthology-based annotation.
- 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. |
| References | - See../bio-skills-references.md |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor 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
-bor-d, never both together. - Verify packaged InterProScan installs have been initialized with
python3 setup.py -f interproscan.propertieswhen required. - Verify required InterProScan helper binaries are resolvable, especially
ps_scan.pl,pfscan, andpfsearch. - 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.