Docs tagged “troubleshooting”

Resolve invalid input, oversized batches, slow queues, and missing scores.

Fix empty results, early stops, unrealistic disconnections, and timeouts.

Troubleshoot API authentication, rate limits, WebSocket/SSE setup, and SDK usage on the platform.

Clear divergences by raising target_accept, read an r_hat_max above 1.01 or a low ess_min, and fix a PK fit whose pk_model or administration is wrong.

Resolve quota errors, payment failures, credit usage, and overage alerts on the platform.

Resolve cache, extension, and browser compatibility issues on the platform.

Troubleshoot canvas card rendering, 3D viewers, exports, and performance on the platform.

Resolve instrument selection failures, convergence issues, LD reference mismatches, and common causal genomics errors.

Resolve design failures, safety prediction issues, manufacturing scoring errors, and KIR matching problems.

Troubleshoot chat streaming, tool calls, citations, and rendering issues on the platform.

Diagnose and resolve streaming failures, tool errors, citation issues, and response quality problems in Ivy.

Four ways to sign in, where settings and the error log live under ~/.config/ivybloom/, what one failed job does to a batch, and how to resume a session.

Why a search returns nothing under the default RECRUITING filter, when to use the generic drug name or full condition term, and NCT ID format errors.

Fixes for timeouts, lost files, missing packages, and stalled downloads in the chat's code workspace.

Resolve guide design failures, excessive off-targets, and CRISPR screen analysis issues.

Fix FlowSOM clusters that split or merge populations, non-reproducible runs without a fixed seed, and FCS files that fail to parse above the 500 MB cap.

Resolve peak calling failures, low signal quality, differential analysis issues, and methylation calling errors.

Fix ESM-3 failures: the 2,048-token window, out-of-memory on long chains, weak embeddings under 30 residues, and similarity that shifts with pooling mode.

Fix a refused file type, the 100 MB and 20-file limits, names caught by the blocked-extension check (results.json contains .js), and proxies blocking S3.

Fix GenMol invalid SMILES, low validity or diversity through temperature and num_steps — plus the known defect that min_qed and max_sa_score never apply.

Resolve query failures, empty results, identifier mismatches, and cross-database linking issues.

Resolve invalid residues, length errors, fetch failures, and stuck jobs.

How to troubleshoot failed, stuck, or unexpected job results on the platform.

Resolve protocol generation errors, experiment submission failures, and result retrieval issues.

Clear a stale Clerk session, fix Google, GitHub or LinkedIn sign-in failures, wait out the 60-minute lock after 5 failed attempts, or check key expiry.

Resolve preprocessing failures, annotation mismatches, differential analysis errors, and pathway enrichment issues.

Resolve classification failures, low-quality results, diversity calculation issues, and differential abundance errors.

Resolve common MM-GBSA force field, parameterization, and energy convergence issues.

Fix connectivity issues, CORS errors, WebSocket failures, and firewalls when using the platform.

Resolve threshold interpretation issues, input format errors, and unexpected results.

Why spacegroup takes a number 1 to 230, not Fm-3m, why Mo K-alpha data scores low against Cu-indexed patterns, and why compute_fingerprint needs a CIF.

Resolve common P2Rank PDB parsing, model selection, and pocket quality issues.

Fix empty PDB searches, invalid or obsolete 4-character IDs, missing HETATM ligands in apo structures, altloc conformations, and RCSB timeouts.

Fix PDB2PQR runs: dropped HETATM ligands and non-standard residues, surprising PROPKA pKa values, DEBUMP clash failures, and timeouts above 10,000 atoms.

Cut chat latency with the thinking budget, drop canvas cards to Tier 1 to free WebGL contexts and memory, and hard-refresh stale bundles after a release.

Resolve linker enumeration failures, ternary complex modeling errors, and degradation scoring issues.

Resolve PRIDE search failures, missing datasets, EMDB query issues, and download problems.

Fix empty PubChem results, synonyms that map to several compounds, structure uploads over 10 MB, and throttling at 5 requests per second or 400 per minute.

Zero results, a 45-second timeout, NCBI rate limits, and the missing abstract that advanced search never fetches — plus why you filter by date, not sort.

Fix a CIF missing _cell_length_a or _atom_site_fract_x, a refinement whose rwp climbs with convergence_flag not 1, and a simulation with peak_count 0.

Resolve reaction SMILES parsing, classification, and condition issues.

Resolve reaction SMILES parsing failures and similarity-search issues.

Resolve GPU memory errors, training convergence issues, input format problems, and model selection questions.

A pre-normalised or logged matrix is refused, not transformed. Also a missing reference label column, mismatched gene names, and Visium HD memory limits.

Resolve infeasible FBA solutions, model construction errors, unexpected growth predictions, and solver failures.

Start here when something breaks — a symptom-to-page router across login, network, jobs, uploads, billing, and the workspaces.

Resolve XTalNet crystal structure prediction and polymorph screening issues.

Fix a missing .nin or .pin index, an out-of-memory run, NCBI 429 throttling on -remote, and an empty hit list — plus when to re-run and when to stop.

Resolve common issues with ChEMBL searches including API errors, rate limits, and data interpretation.

No results or the wrong protein? Name the right organism or drop it, check for a retired accession, and ask for the sequence when it is missing.