Codex couldn't start because its local database appears to be damaged.

[pshah-nv]

What version of Codex CLI is running?

OpenAI Codex (v0.149.1)

What subscription do you have?

Enterprise

Which model were you using?

gpt-5.6-terra medium

What platform is your computer?

Linux 6.1.62-4.x86_64 x86_64 x86_64

What terminal emulator and version are you using (if applicable)?

MATE Terminal

Codex doctor report

pdx4-sim-a06-003:/home/scratch.pshah_cpu/other/ai/codex> codex doctor --json
WARNING: failed to clean up stale arg0 temp dirs: Directory not empty (os error 39)
{
  "schemaVersion": 1,
  "generatedAt": "1787679622s since unix epoch",
  "overallStatus": "fail",
  "codexVersion": "0.149.1",
  "checks": {
    "app_server.status": {
      "id": "app_server.status",
      "category": "app-server",
      "status": "warning",
      "summary": "background server socket is stale or unreachable",
      "details": {
        "app-server version": "unavailable (failed to connect to control socket)",
        "control socket": "/home/pshah/.codex/app-server-control/app-server-control.sock",
        "daemon state dir": "/home/pshah/.codex/app-server-daemon",
        "mode": "ephemeral",
        "pid file": "/home/pshah/.codex/app-server-daemon/app-server.pid (missing)",
        "settings": "/home/pshah/.codex/app-server-daemon/settings.json (missing)",
        "status": "stale or unreachable",
        "update-loop pid file": "/home/pshah/.codex/app-server-daemon/app-server-updater.pid (missing)"
      },
      "remediation": "Run codex app-server daemon version for more details.",
      "durationMs": 2
    },
    "auth.credentials": {
      "id": "auth.credentials",
      "category": "auth",
      "status": "ok",
      "summary": "auth is configured",
      "details": {
        "auth file": "/home/pshah/.codex/auth.json",
        "auth storage mode": "File",
        "stored API key": "false",
        "stored ChatGPT tokens": "true",
        "stored agent identity": "false",
        "stored auth mode": "chatgpt"
      },
      "remediation": null,
      "durationMs": 0
    },
    "config.load": {
      "id": "config.load",
      "category": "config",
      "status": "ok",
      "summary": "config loaded",
      "details": {
        "CODEX_HOME": "/home/pshah/.codex",
        "config.toml": "/home/pshah/.codex/config.toml",
        "config.toml parse": "ok",
        "cwd": "/home/scratch.pshah_cpu/other/ai/codex",
        "enabled feature flags": "shell_tool, view_image, unified_exec, shell_snapshot, code_mode_host, terminal_resize_reflow, sqlite, hooks, enable_request_compression, unbounded_connection_retries, multi_agent, apps, tool_search_always_defer_mcp_tools, tool_suggest, plugins, in_app_browser, in_app_chat, in_app_dictation, in_app_updates, browser_use, browser_use_full_cdp_access, browser_use_external, computer_use, remote_plugin, plugin_sharing, image_generation, resize_all_images, item_ids, skill_mcp_dependency_install, skill_search, mentions_v2, steer, guardian_approval, goals, collaboration_modes, tool_call_mcp_elicitation, auth_elicitation, personality, fast_mode, tui_app_server, remote_compaction_v2, workspace_dependencies",
        "feature flag overrides": "none",
        "feature flags enabled": "42",
        "log dir": "/home/pshah/.codex/log",
        "mcp servers": "13",
        "model": "gpt-5.6-terra",
        "model provider": "openai",
        "sqlite home": "/home/pshah/.codex"
      },
      "remediation": null,
      "durationMs": 0
    },
    "git.environment": {
      "id": "git.environment",
      "category": "git",
      "status": "ok",
      "summary": "git version 2.39.3",
      "details": {
        "PATH git #1": "/bin/git",
        "PATH git #2": "/usr/bin/git",
        "PATH git entries": "2",
        "git build options": "git version 2.39.3; cpu: x86_64; no commit associated with this build; sizeof-long: 8; sizeof-size_t: 8; shell-path: /bin/sh",
        "git exec path": "/usr/libexec/git-core",
        "git version": "git version 2.39.3",
        "repo detected": "false",
        "selected git": "/bin/git"
      },
      "remediation": null,
      "durationMs": 97
    },
    "installation": {
      "id": "installation",
      "category": "install",
      "status": "warning",
      "summary": "npm-managed launch could not inspect npm global root",
      "details": {
        "PATH codex #1": "/home/tools_ai/openai/codex/latest/bin/codex",
        "current executable": "/home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
        "install context": "npm (package /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
        "managed by bun": "false",
        "managed by npm": "true",
        "managed by pnpm": "false",
        "managed package root": "/home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex",
        "npm root -g failed": "No such file or directory (os error 2)"
      },
      "remediation": null,
      "durationMs": 117
    },
    "mcp.config": {
      "id": "mcp.config",
      "category": "mcp",
      "status": "warning",
      "summary": "MCP configuration has optional issues",
      "details": {
        "configured servers": "13",
        "disabled servers": "0",
        "optional reachability failed": "maas_nvbugs: https://maas.prd.astra.nvidia.com/maas/<redacted> (HEAD request timed out; GET request timed out)",
        "streamable_http servers": "13"
      },
      "remediation": "Set the missing MCP env vars or disable the affected server.",
      "durationMs": 9728
    },
    "network.env": {
      "id": "network.env",
      "category": "network",
      "status": "ok",
      "summary": "network-related environment looks readable",
      "details": {
        "managed proxy": "not configured",
        "proxy env vars": "none",
        "respect system proxy": "disabled"
      },
      "remediation": null,
      "durationMs": 0
    },
    "network.provider_reachability": {
      "id": "network.provider_reachability",
      "category": "reachability",
      "status": "ok",
      "summary": "active provider endpoints are reachable over HTTP",
      "details": {
        "ChatGPT inference URL": "https://chatgpt.com/backend-api/<redacted> reachable (HTTP 405)",
        "reachability mode": "ChatGPT auth"
      },
      "remediation": null,
      "durationMs": 232
    },
    "network.websocket_reachability": {
      "id": "network.websocket_reachability",
      "category": "websocket",
      "status": "ok",
      "summary": "Responses WebSocket handshake succeeded",
      "details": {
        "DNS": "2 IPv4, 2 IPv6, first IPv4",
        "auth mode": "chatgpt",
        "connect timeout": "15000 ms",
        "endpoint": "wss://chatgpt.com/backend-api/<redacted>",
        "handshake result": "HTTP 101 Switching Protocols",
        "model provider": "openai",
        "provider name": "OpenAI",
        "proxy env vars": "none",
        "reasoning header": "false",
        "server model present": "false",
        "supports websockets": "true",
        "wire API": "responses"
      },
      "remediation": null,
      "durationMs": 755
    },
    "runtime.provenance": {
      "id": "runtime.provenance",
      "category": "runtime",
      "status": "ok",
      "summary": "running npm on linux-x86_64",
      "details": {
        "commit": "unknown",
        "current executable": "/home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
        "install method": "npm (package /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
        "platform": "linux-x86_64",
        "version": "0.149.1"
      },
      "remediation": null,
      "durationMs": 0
    },
    "runtime.search": {
      "id": "runtime.search",
      "category": "search",
      "status": "ok",
      "summary": "search is OK (bundled)",
      "details": {
        "search command": "/home/tools_ai/openai/codex/0.149.1/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path/rg",
        "search command readiness": "file exists",
        "search provider": "bundled"
      },
      "remediation": null,
      "durationMs": 0
    },
    "sandbox.helpers": {
      "id": "sandbox.helpers",
      "category": "sandbox",
      "status": "ok",
      "summary": "sandbox configuration is readable",
      "details": {
        "approval policy": "OnRequest",
        "codex-linux-sandbox helper": "/home/pshah/.codex/tmp/arg0/codex-arg03XShtg/codex-linux-sandbox",
        "execve wrapper helper": "/home/pshah/.codex/tmp/arg0/codex-arg03XShtg/codex-execve-wrapper",
        "filesystem sandbox": "restricted",
        "network sandbox": "restricted"
      },
      "remediation": null,
      "durationMs": 0
    },
    "security.endpoint": {
      "id": "security.endpoint",
      "category": "security",
      "status": "ok",
      "summary": "endpoint protection is not inspected on this platform",
      "details": {
        "endpoint products": "not inspected on this platform"
      },
      "remediation": null,
      "durationMs": 0
    },
    "state.paths": {
      "id": "state.paths",
      "category": "state",
      "status": "fail",
      "summary": "state database integrity check failed",
      "details": {
        "CODEX_HOME": "/home/pshah/.codex (dir)",
        "active rollout files": "50 files, 492007913 total bytes, 9840158 average bytes",
        "archived rollout files": "3 files, 19326360 total bytes, 6442120 average bytes",
        "goals DB": "/home/pshah/.codex/goals_1.sqlite (file)",
        "goals DB integrity": "ok",
        "log DB": "/home/pshah/.codex/logs_2.sqlite (file)",
        "log DB integrity": "*** in database main ***\nTree 5 page 5 right child: invalid page number 446\nTree 5 page 5 right child: invalid page number 445\nTree 5 page 5 right child: invalid page number 443\nTree 5 page 5 right child: invalid page number 442\nTree 5 page 5 right child: invalid page number 440\nTree 5 page 5 right child: invalid page number 437\nTree 5 page 5 right child: invalid page number 436\nTree 5 page 5 right child: invalid page number 435\nTree 5 page 5 right child: invalid page number 433\nTree 5 page 5 right child: invalid page number 432\nTree 5 page 5 right child: invalid page number 431\nTree 5 page 5 right child: invalid page number 429\nTree 5 page 5 right child: invalid page number 428\nTree 5 page 5 right child: invalid page number 427\nTree 5 page 5 right child: invalid page number 426\nTree 5 page 5 right child: invalid page number 425\nTree 5 page 5 right child: invalid page number 424\nTree 5 page 5 right child: invalid page number 423\nTree 5 page 5 right child: invalid page number 422\nTree 5 page 5 right child: invalid page number 421\nTree 5 page 5 right child: invalid page number 420\nTree 5 page 5 right child: invalid page number 419\nTree 5 page 5 right child: invalid page number 418\nTree 5 page 5 right child: invalid page number 416\nTree 5 page 5 right child: invalid page number 415\nTree 5 page 5 right child: invalid page number 414\nTree 5 page 5 right child: invalid page number 413\nTree 5 page 5 right child: invalid page number 412\nTree 5 page 5 right child: invalid page number 411\nTree 5 page 5 right child: invalid page number 410\nTree 5 page 5 right child: invalid page number 409\nTree 5 page 5 right child: invalid page number 408\nTree 5 page 5 right child: invalid page number 407\nTree 5 page 5 right child: invalid page number 406\nTree 5 page 5 right child: invalid page number 405\nTree 5 page 5 right child: invalid page number 403\nTree 5 page 5 right child: invalid page number 401\nTree 5 page 5 right child: invalid page number 400\nTree 5 page 5 right child: invalid page number 399\nTree 5 page 5 right child: invalid page number 397\nTree 5 page 5 right child: invalid page number 396\nTree 5 page 5 right child: invalid page number 395\nTree 5 page 5 right child: invalid page number 394\nTree 5 page 5 right child: invalid page number 393\nTree 5 page 5 right child: invalid page number 392\nTree 5 page 5 right child: invalid page number 391\nTree 5 page 5 right child: invalid page number 390\nTree 5 page 5 right child: invalid page number 388\nTree 5 page 5 right child: invalid page number 387\nTree 5 page 5 right child: invalid page number 386\nTree 5 page 5 right child: invalid page number 385\nTree 5 page 5 right child: invalid page number 384\nTree 5 page 5 right child: invalid page number 383\nTree 5 page 5 right child: invalid page number 382\nTree 5 page 5 right child: invalid page number 381\nTree 5 page 5 right child: invalid page number 380\nTree 5 page 5 right child: invalid page number 379\nTree 5 page 5 right child: invalid page number 378\nTree 5 page 5 right child: invalid page number 377\nTree 5 page 5 right child: invalid page number 375\nTree 5 page 5 right child: invalid page number 374\nTree 5 page 5 right child: invalid page number 373\nTree 5 page 5 right child: invalid page number 372\nTree 5 page 5 right child: invalid page number 370\nTree 5 page 5 right child: invalid page number 369\nTree 5 page 5 right child: invalid page number 368\nTree 5 page 5 right child: invalid page number 367\nTree 5 page 5 right child: invalid page number 366\nTree 5 page 5 right child: invalid page number 365\nTree 5 page 5 right child: invalid page number 364\nTree 5 page 5 right child: invalid page number 363\nTree 5 page 5 right child: invalid page number 360\nTree 5 page 5 right child: invalid page number 359\nTree 5 page 5 right child: invalid page number 358\nTree 5 page 5 right child: invalid page number 357\nTree 5 page 5 right child: invalid page number 356\nTree 5 page 5 right child: invalid page number 355\nTree 5 page 5 right child: invalid page number 354\nTree 5 page 5 right child: invalid page number 353\nTree 5 page 5 right child: invalid page number 352\nTree 5 page 5 right child: invalid page number 351\nTree 5 page 5 right child: invalid page number 350\nTree 5 page 5 right child: invalid page number 349\nTree 5 page 5 right child: invalid page number 348\nTree 5 page 5 right child: invalid page number 347\nTree 5 page 5 right child: invalid page number 346\nTree 5 page 5 right child: invalid page number 344\nTree 5 page 5 right child: invalid page number 343\nTree 5 page 5 right child: invalid page number 342\nTree 5 page 5 right child: invalid page number 341\nTree 5 page 5 right child: invalid page number 340\nTree 5 page 5 right child: invalid page number 339\nTree 5 page 5 right child: invalid page number 338\nTree 5 page 5 right child: invalid page number 337\nTree 5 page 5 right child: invalid page number 335\nTree 5 page 5 right child: invalid page number 334\nTree 5 page 5 right child: invalid page number 333\nTree 5 page 5 right child: invalid page number 332\nTree 5 page 5 right child: invalid page number 330\nTree 5 page 5 right child: invalid page number 329",
        "log dir": "/home/pshah/.codex/log (dir)",
        "memories DB": "/home/pshah/.codex/memories_1.sqlite (file)",
        "memories DB integrity": "ok",
        "queue DB": "/home/pshah/.codex/queue_1.sqlite (file)",
        "queue DB integrity": "ok",
        "sqlite home": "/home/pshah/.codex (dir)",
        "state DB": "/home/pshah/.codex/state_5.sqlite (file)",
        "state DB integrity": "ok",
        "thread history DB": "/home/pshah/.codex/thread_history_1.sqlite (file)",
        "thread history DB integrity": "ok"
      },
      "remediation": "Move the damaged SQLite database aside, then restart the interactive CLI or app server so it can rebuild that runtime database from saved data. Other entry points may not rebuild automatically.",
      "durationMs": 1142
    },
    "state.rollout_db_parity": {
      "id": "state.rollout_db_parity",
      "category": "threads",
      "status": "ok",
      "summary": "rollout files and state DB thread inventory agree",
      "details": {
        "default model provider": "openai",
        "rollout DB active files": "50",
        "rollout DB active rows": "50",
        "rollout DB archive mismatches": "0",
        "rollout DB archived files": "3",
        "rollout DB archived rows": "3",
        "rollout DB duplicate DB paths": "0",
        "rollout DB duplicate rollout thread ids": "0",
        "rollout DB malformed file names": "0",
        "rollout DB missing active rows": "0",
        "rollout DB missing archived rows": "0",
        "rollout DB model providers": "openai=53",
        "rollout DB rows": "53",
        "rollout DB scan cap reached": "false",
        "rollout DB scan errors": "0",
        "rollout DB sources": "subagent:other=39, cli=7, vscode=7",
        "rollout DB stale rows": "0"
      },
      "remediation": null,
      "durationMs": 415
    },
    "system.disk": {
      "id": "system.disk",
      "category": "disk",
      "status": "warning",
      "summary": "low disk space (3.4 GiB)",
      "details": {
        "CODEX_HOME available": "3.4 GiB",
        "failure threshold": "1.0 GiB",
        "warning threshold": "5.0 GiB",
        "worktree available": "2378.9 GiB"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "CODEX_HOME has insufficient disk space",
          "measured": "3.4 GiB",
          "expected": "at least 5.0 GiB",
          "remedy": "Free disk space or move the worktree to a larger volume.",
          "fields": [
            "CODEX_HOME available"
          ]
        }
      ],
      "remediation": null,
      "durationMs": 0
    },
    "system.environment": {
      "id": "system.environment",
      "category": "system",
      "status": "ok",
      "summary": "OS language en-US",
      "details": {
        "EDITOR": "set",
        "LANG": "en_US.utf8",
        "LC_ALL": "en_US.utf8",
        "LC_CTYPE": "en_US.utf8",
        "VISUAL": "not set",
        "os": "Rocky Linux 8.9.0 [64-bit]",
        "os language": "en-US",
        "os type": "Rocky Linux",
        "os version": "8.9.0"
      },
      "remediation": null,
      "durationMs": 43
    },
    "terminal.env": {
      "id": "terminal.env",
      "category": "terminal",
      "status": "ok",
      "summary": "terminal metadata was detected",
      "details": {
        "DISPLAY": "present",
        "SSH_CLIENT": "present",
        "SSH_CONNECTION": "present",
        "SSH_TTY": "present",
        "TERM": "xterm",
        "color output": "enabled",
        "effective locale": "en_US.utf8",
        "stderr is terminal": "true",
        "stdin is terminal": "true",
        "stdout is terminal": "true",
        "terminal": "unknown",
        "terminal size": "128x50"
      },
      "remediation": null,
      "durationMs": 0
    },
    "terminal.title": {
      "id": "terminal.title",
      "category": "title",
      "status": "ok",
      "summary": "terminal title default",
      "details": {
        "terminal title activity": "true",
        "terminal title items": "activity, project-name",
        "terminal title project source": "project config",
        "terminal title project value": "codex",
        "terminal title source": "default"
      },
      "remediation": null,
      "durationMs": 0
    },
    "updates.status": {
      "id": "updates.status",
      "category": "updates",
      "status": "warning",
      "summary": "npm update target could not be inspected",
      "details": {
        "cached latest version": "0.149.0",
        "check for update on startup": "true",
        "last checked at": "2026-08-21T16:29:32.902704596Z",
        "latest version probe": "curl: (22) The requested URL returned error: 403",
        "npm root -g failed": "No such file or directory (os error 2)",
        "update action": "npm install -g @openai/codex",
        "version cache": "/home/pshah/.codex/version.json"
      },
      "remediation": null,
      "durationMs": 42
    }
  }

What issue are you seeing?

pdx4-sim-a06-003:/home/scratch.pshah_cpu/other/ai/codex> qsub -q o_cpu_idle_64G -Is codex -s workspace-write -a on-request resume 019f8f60-c8bd-7632-b8aa-d5fb8b87ec50
Job <1697616912> is submitted to queue <o_pri_interactive>.
<<Waiting for dispatch ...>>
<>
╭───────────────────────────────────────────────────╮
│ >_ OpenAI Codex (v0.149.1) │
│ │
│ model: loading /model to change │
│ directory: /home/scratch.pshah_cpu/other/ai/codex │
╰───────────────────────────────────────────────────╯
Resuming session…

› [<1u [<u [>4;0mCodex couldn't start because its local database appears to be damaged.
Moving the damaged local database aside so Codex can rebuild it from saved data.
Technical details:
Location: /home/pshah/.codex/state_5.sqlite
Cause: failed to initialize state runtime at /home/pshah/.codex: error returned from database: (code: 11) database disk image is malformed: (code: 11) database disk image is malformed
Codex rebuilt its local database.
Codex detected a damaged local database, moved it into a backup folder, and will continue startup with a fresh database.
Database path: /home/pshah/.codex/state_5.sqlite
Backup folder: /home/pshah/.codex/db-backups/sqlite-1787676319-0
Press Enter to continue.

What steps can reproduce the bug?

Uploaded thread: 019f8f60-c8bd-7632-b8aa-d5fb8b87ec50

What is the expected behavior?

No database corruption

Additional information

No response

[pshah-nv]

Note the session does resume, but I get this error every time.

[github-actions]

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• Desktop (Windows): corrupt logs_2.sqlite B-tree causes a deterministic, unrecoverable app-server handshake timeout #39015

Powered by Codex Action