GraphSol job sizing and limits

This page helps you size GraphSol submissions for predictable runtimes and stay within input limits. Sequence length, batch size, and threshold choice matter most for what runs cleanly and how you read the results.

GraphSol job sizing and limits

Plan submissions to stay within recommended limits and predictable runtimes.

Input limits

• Sequences: 20–4,096 residues each.
• File size: ≤ 25 MB (compressed .gz accepted).
• Character set: 20 standard amino acids; other symbols are stripped with warnings.
• Unique IDs: duplicate headers are deduplicated unless you set skipDeduplication.

Batch sizing

• Small sets (<500 sequences): single batch is fastest; expect ~5 minutes.
• Medium (500–5,000): keep in one file; runtime scales roughly linearly.
• Large (>5,000): split into multiple jobs to avoid timeouts and simplify retries.

Threshold guidance

• Default: 0.5 balances precision/recall.
• Precision-first: 0.6–0.7.
• Recall-first: 0.3–0.4.
• You can re-threshold offline from results.csv without rerunning the model.

Runtime expectations

• Most jobs return within 5–12 minutes depending on batch size.
• Poll every 5–10 seconds; long polls reduce load without slowing delivery.
• If a job exceeds 20 minutes for <5,000 sequences, retry with smaller batches.

Resubmission hygiene

• Keep original FASTA and summary.json side by side for auditing.
• When retrying, update headers to avoid accidental deduplication, or disable it explicitly.
• Capture jobId, submission timestamp, and threshold in logs for reproducibility.