GraphSol troubleshooting

This page helps you diagnose the issues that most often interrupt a GraphSol run — invalid residues, out-of-range sequence lengths, duplicate IDs, failed UniProt fetches, and jobs stuck in running — plus the quality checks to run before scaling up. GraphSol builds a graph from a predicted contact map, so most failures trace back to sequence integrity rather than the model itself.

Input and validation errors

• "Invalid residues": one or more sequences contain non-standard characters. Clean inputs to the 20-letter amino-acid alphabet (ACDEFGHIKLMNPQRSTVWY); remove ambiguous codes (B, J, O, U, X, Z).
• "Sequence too long/short": keep sequences between 20 and 4,096 residues. Split very long chains into domains, or check for a concatenation/translation-frame error on the shorter ones.
• "Duplicate IDs detected": use unique FASTA headers, or disable deduplication explicitly if the duplicates are intentional controls.
• File rejected on upload: keep files under 25 MB; gzip (.gz) is auto-detected. Split larger libraries into multiple jobs. See preparing inputs.

UniProt fetch failures

• When you submit by UniProt ID, the sequence is fetched automatically; an unknown or malformed accession will fail that row.
• Verify the accession format (for example P00533) and that it resolves on UniProt before submitting.
• If a fetch is flaky, paste the FASTA sequence directly instead.

Job stuck in running

• Check network stability and retry status polling with backoff; large batches can take several minutes.
• Feature generation (contact-map and profile features) is the heavy step — very large batches spend most of their time there.
• If a job exceeds 20 minutes for fewer than 5,000 sequences, treat it as a candidate ticket rather than continuing to wait.

Quality checks

• Compare summary.json counts to your original file to confirm every sequence was processed.
• Scan the warnings column in results.csv for trimmed or filtered inputs.
• Re-run a small subset (5–10 sequences) to validate inputs before scaling to full batches.

Interpreting borderline scores

• GraphSol returns a per-sequence probability (0–1) plus a binary call at a 0.5 default threshold; scores near 0.5 are genuinely ambiguous, not errors.
• For a consensus view, run DeepSol on the same sequences — the two use different methods, so agreement raises confidence.
• Probabilities that appear constant across many diverse sequences point to an input problem (for example, every sequence failing feature generation), not real biology.

When to contact support

• Repeated failures with clean FASTA files.
• Jobs exceeding 20 minutes for fewer than 5,000 sequences.
• Probability outputs that appear constant across many diverse sequences.

Include the jobId, submission time, and whether the input was gzipped when opening a ticket.

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