Why a DeepSol job rejects a sequence, times out or returns low confidence — ambiguous residues such as X or B, oversized batches, membrane proteins.

This page helps you diagnose the problems that most often surface with DeepSol — invalid sequence characters, slow or timing-out batches, unexpectedly low confidence, and predictions that don't match experimental results.

Common issues and fixes

Invalid sequence errors

Ensure sequences contain only standard amino acid characters (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).
Remove any ambiguous residues (X, B, Z, J) or replace with the most likely amino acid.
Check for numerical characters, spaces, or special symbols in your sequences.
For FASTA uploads, verify header lines start with > and sequences are on subsequent lines.

Timeouts or slow batches

Reduce batchSize to 16 or smaller for very long protein sequences.
Chunk large sequence libraries to under ~1,000 records per submission.
Retry on 429 or 503 with exponential backoff and a small jitter.
Consider splitting very long proteins (>2000 residues) into domains if biologically appropriate.

Unexpectedly low confidence

Check warnings for domain-fit notes; the CNN may be uncertain for unusual sequences.
Verify sequence length is within the optimal range (50-2000 residues).
Membrane proteins, intrinsically disordered regions, and unusual amino acid compositions may yield lower confidence.
If the protein class is far from typical E. coli-expressed proteins, treat predictions as qualitative guidance only.

Predictions don't match experimental results

Remember DeepSol achieves 77% accuracy (MCC 0.55); some predictions will be incorrect.
Expression conditions significantly affect actual solubility (temperature, IPTG concentration, media, strain).
The model predicts intrinsic solubility tendency; fusion tags and chaperones can improve outcomes.
Consider the experimental context: were inclusion bodies observed, or was protein simply not detected?

Missing identifiers in outputs

Include descriptive FASTA headers or an id column in CSV uploads; these are echoed back unchanged.
When submitting multiple identical sequences, results will be deduplicated by default.

Sequence formatting issues

Remove line breaks within sequences (sequences should be continuous).
Ensure consistent case (uppercase preferred, but lowercase is accepted).
Strip any sequence numbering or annotation characters.
Verify UTF-8 encoding for uploaded files.

Still stuck?

Capture the failing input sequences and job ID, then contact support with timestamps and workspace ID.
Include whether you used FASTA, raw sequence, or CSV format and the chosen batchSize.
Note any specific error messages or warnings returned by the system.

DeepSol troubleshooting