When a DeepAgents tool is missing, first check which middleware and harness profile expose it. When a tool is visible but fails, check the configured backend and the path, permissions, and container context it uses. In particular, execute requires a sandbox-capable backend; running the agent in Docker does not make a storage backend capable of executing commands.
Start by identifying what failed
Record the exact tool name and arguments, the complete error or traceback, the agent configuration, and the installed DeepAgents and related package versions. Then classify the symptom:
- Tool missing: the model was not offered the tool. Investigate middleware and harness configuration.
- Tool call failed: the tool was offered, but its backend or execution environment could not complete the request. Investigate backend capability, paths, permissions, and container context.
DeepAgents’ overview and agent architecture describe middleware around model calls and tool execution. Middleware can add or remove tools, so an error from a tool call and the absence of that tool are not the same problem.
If a tool is missing, inspect middleware and profiles
Check the middleware supplied when constructing the agent and any harness profile exclusions. The current project overview lists filesystem tools as middleware-provided and presents execute as available with sandbox backends. A profile can exclude filesystem tools from the model’s visible tool list.
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Do not interpret a permission denial as proof that a tool is absent. DeepAgents documents ordered filesystem permission rules for its built-in filesystem tools; a tool may be visible and then denied or interrupted when called. The overview also distinguishes those built-in tool permissions from arbitrary command execution through sandbox backends.
If execute is unavailable, verify the backend
Inspect the actual backend instance passed to the agent. DeepAgents’ default state or storage backend is not, by itself, a shell execution environment. The filesystem middleware checks whether its backend supports the sandbox execution protocol and can return an explicit error if it does not. Putting the agent process in a Docker container does not turn a regular storage backend into an execution backend.
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- Confirm which backend object the agent actually receives; do not rely only on a class name or a Docker deployment description.
- Check whether that backend implements the sandbox execution protocol required by the installed DeepAgents release.
- Compare the installed DeepAgents and backend package versions with the compatibility requirements in the project overview and filesystem middleware implementation. APIs and supported protocol versions can change, so validate older examples against your installed release.
If a call fails in Docker, check the execution context
A tool’s paths and commands must make sense where the backend executes them—not merely on the host or in the agent’s own container. Verify that the target container is running, that the requested command exists and is executable in its image, and that the backend is targeting the intended container.
- Check that the configured working directory exists inside the execution container.
- Check that paths passed to filesystem operations are valid in the backend’s container or virtual namespace.
- Compare the tool arguments with the paths and executable locations available in the target image.
A user-submitted issue titled “SandboxBackend.grep crashes with ValueError when container exec fails” reports a grep parsing crash after the sandbox work directory was missing inside the container. The report identifies DeepAgents 0.6.1, Python 3.12, and a Linux host. It is a specific reproduction, not evidence that every release has the same defect; first verify whether your configured directory exists and whether your installed version is affected.
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Trace network failures from the process making the connection
Identify whether the connection originates from the host process, the agent container, or a separate sandbox container. Record the destination, port, and complete connection error, then test reachability from that same environment. A successful connection from the host does not establish that a separate execution container can reach the same destination.
The available DeepAgents documentation and deployment guide do not establish one universal Docker networking fix. Diagnose the actual source process and destination rather than changing network modes on the assumption that all tool failures share a cause.
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Keep filesystem permissions separate from shell security
The DeepAgents overview says filesystem permission rules apply to its built-in filesystem tools, but not to sandbox backends that allow arbitrary command execution. Those rules should not be treated as a security boundary for shell commands. Use controls at the backend and deployment level, and consult current official security guidance before allowing untrusted inputs to trigger execution.
When to consider a managed sandbox
DeepAgents’ sandbox deployment guide describes provider choices and lifecycle scopes, including thread- and assistant-level options. It does not establish a general winner for security, price, reliability, or performance. Compare the concrete requirements that affect your deployment:
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- Where commands execute and what isolation boundary the provider supplies.
- How long the environment and its files persist, and whether lifecycle is scoped to a thread or assistant.
- How files and credentials are made available to the execution environment.
- How much control you need over images, installed packages, and network configuration.
Check current provider documentation for availability and configuration details before choosing a managed service.
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