> ## Documentation Index
> Fetch the complete documentation index at: https://docs.synthesize.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Troubleshooting

> Fix common connection, authentication, and analysis-expectation issues when using Synthesize Bio MCP.

# Troubleshooting

## Claude cannot connect to the connector

Confirm that you selected the Synthesize Bio Claude Connector from
[Claude's connector marketplace](https://claude.ai/settings/connectors).

Also confirm that:

* the connector was saved successfully in Claude
* you completed the OAuth sign-in flow
* your Synthesize Bio account has access to the platform

## The analysis is taking a long time

This is usually expected. Most runs take about 3 to 5 minutes. Synthesize Bio MCP is designed to run asynchronously, so Claude may need to wait and poll for progress before it can return the final result.

## The user expected more than one comparison

The current workflow supports one pairwise comparison per run. If a prompt implies more than two groups, the current behavior compares the first two groups alphabetically.

If a user needs several comparisons, run them as separate prompts.

## The result is too technical

Ask Claude to summarize the output in simpler language, or ask for a focused interpretation such as:

* the most important up-regulated genes
* the most important down-regulated genes
* likely biological pathways or mechanisms

## The user wants the most detailed output

Ask Claude for the structured JSON output or the full technical details from the completed run.

## Still need help

See [Privacy and Support](./privacy-and-support) for support contact options.