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Troubleshooting

  • Rate limit responses include retry information; wait or provide your own LLM.
  • Verify preprocessing: clustering and rank_genes_groups must be present.
  • Make sure you have valid gene symbols in the AnnData object and are passing the correct gene symbols column name to parameter gene_symbols_column.
  • If you are using a custom LLM, make sure you have the correct API key and base URL.
  • For large datasets, load AnnData in backed mode (sc.read_h5ad(..., backed="r")) to reduce memory use during artifact generation.
  • run() creates vars.h5 and obs.duckdb before annotation. Use cleanup_artifacts=True if you do not want to keep these local files.
  • If artifact building or uploading fails, run() will raise an error by default. Set require_artifacts=False to skip artifacts and continue with annotation only.