Borrowing it
Nothing to install: this file belongs to cafferychen777/ChatSpatial. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/cafferychen777/ChatSpatial/main/.agents/skills/troubleshoot/SKILL.mdgit clone --depth 1 https://github.com/cafferychen777/ChatSpatialWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/cafferychen777/chatspatial/troubleshoot)<a href="https://agentmods.dev/skills/cafferychen777/chatspatial/troubleshoot"><img src="https://agentmods.dev/badge/skills/cafferychen777/chatspatial/troubleshoot/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/cafferychen777/chatspatial/troubleshoot"><img src="https://agentmods.dev/badge/skills/cafferychen777/chatspatial/troubleshoot.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00065 | $0.01738 |
| Opus 5 | $0.00032 | $0.00869 |
| Sonnet 5 | $0.00013 | $0.00348 |
| Haiku 4.5 | $0.00006 | $0.00174 |
Grade A, and why
troubleshoot scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 284 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Troubleshooting Guide
Overview
This skill helps diagnose and resolve common issues in ChatSpatial analysis.
Quick Diagnosis Tree
Q: What type of problem?
│
├─ Analysis fails with error
│ └─ See: Error Messages section
│
├─ Analysis runs but results look wrong
│ └─ See: Result Validation section
│
├─ Performance issues (slow/memory)
│ └─ See: Performance section
│
└─ Dependency/installation problems
└─ See: Environment section
Error Messages
Data Loading Errors
| Error | Cause | Solution |
|---|---|---|
FileNotFoundError |
Path incorrect | Verify file path exists |
KeyError: 'spatial' |
No spatial coordinates | Check data format, use correct loader |
ValueError: sparse matrix |
Format mismatch | Convert to compatible format |
MemoryError |
File too large | Use chunked loading or subsample |
Diagnostic steps:
1. Verify file exists: ls -la <path>
2. Check file size: du -h <path>
3. Try reading header only to test format
Preprocessing Errors
| Error | Cause | Solution |
|---|---|---|
No highly variable genes |
Filtering too strict | Lower min_mean/max_mean thresholds |
Negative values after log |
Data not normalized | Use raw counts first |
Empty AnnData after QC |
QC too strict | Relax min_genes/min_cells |
Method-Specific Errors
Deconvolution
| Error | Cause | Solution |
|---|---|---|
No shared genes |
Reference mismatch | Check gene naming (symbols vs IDs) |
RCTD failed |
R/rpy2 issue | Verify R installation, check rpy2 |
Cell2location GPU error |
CUDA issue | Use CPU mode, check GPU availability |
Reference cell types missing |
Bad annotation column | Verify cell_type_key exists |
Cell Communication
| Error | Cause | Solution |
|---|---|---|
CellChat R error |
R dependency | Install CellChat in R first |
No interactions found |
Stringent filtering | Lower p-value threshold |
Species database not found |
Wrong species config | Use "human" or "mouse" |
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 11d ago First seen · 284 lines · 65 tokens per session scan A 338c764ffb10
troubleshoot is a skill published in the GitHub repository cafferychen777/ChatSpatial (44 stars, last pushed 26d ago), licensed MIT. It adds 65 tokens to every session and 1,738 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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