CATOCATO

Troubleshooting

Solutions for common issues you may encounter while using CATO.

Upload fails or times out

Symptoms

  • •Error message "Upload failed" appears
  • •Progress bar stops before completing
  • •Browser shows timeout error

Solutions

  1. Check that your file is under your plan's size limit: Free (25 MB), Base (100 MB), Pro (500 MB), Pay-as-you-go (1 GB), Enterprise (Unlimited)
  2. Verify the file format is supported (.csv, .tsv, .xlsx, .xls, .json, .parquet, .h5, .fcs, .sas7bdat, .dta, .pdf, .zip, .tar)
  3. For .xls (legacy Excel) files, ensure the file is not corrupted — CATO uses xlrd for legacy Excel support
  4. Ensure you have a stable internet connection
  5. Try uploading a smaller test file to isolate the issue
  6. For ZIP/TAR archives, ensure the decompressed size is under 2 GB
  7. Clear your browser cache and try again

Data preview shows incorrect characters

Symptoms

  • •Special characters display as question marks or boxes
  • •Accented characters are garbled
  • •Column names contain strange symbols

Solutions

  1. Re-save your file with UTF-8 encoding in your spreadsheet application
  2. In Excel: File → Save As → Choose CSV UTF-8 (Comma delimited)
  3. Avoid copying data from PDFs or legacy systems without cleaning
  4. Remove any special characters that are not standard UTF-8

CATO Chat returns unexpected results

Symptoms

  • •Results do not match expected values
  • •CATO references wrong columns or datasets
  • •Summary statistics seem incorrect

Solutions

  1. Use @-mentions to reference the exact dataset you want to query
  2. Check column names for typos or case sensitivity issues
  3. Review your data for unexpected null values or outliers
  4. Start a new chat session to clear context
  5. Use Plan mode (Shift+Tab) so CATO outlines its approach before executing

Visualizations not appearing in the side panel

Symptoms

  • •CATO says it created a visualization but nothing appears
  • •Visualization panel shows "No visualizations yet"
  • •Figures appear inline but not in the gallery panel

Solutions

  1. Refresh the page and reopen the conversation — figures should persist
  2. Click the Visualizations panel toggle button to ensure it is open
  3. Check that the chat session loaded completely (wait for streaming to finish)
  4. Try asking CATO to generate the visualization again
  5. Clear your browser cache and reload the page

File artifacts cannot be downloaded

Symptoms

  • •Download button does not respond
  • •File downloads but is empty or corrupted
  • •File artifact card shows but has no download option

Solutions

  1. Ensure pop-ups and downloads are not blocked by your browser
  2. Try right-clicking the download button and selecting "Save link as"
  3. Ask CATO to regenerate the file if the original was from a previous session
  4. Check your browser's download folder for the file

Page does not load or is blank

Symptoms

  • •White screen after login
  • •Infinite loading spinner
  • •Error message in browser console

Solutions

  1. Refresh the page (Ctrl/⌘ + R)
  2. Clear browser cache and cookies
  3. Try a different browser (Chrome or Firefox recommended)
  4. Disable browser extensions that may interfere
  5. Check if your browser is up to date

Literature search returns no results

Symptoms

  • •Search completes but shows zero results
  • •Results grid is empty after running a query
  • •"No publications found" message appears

Solutions

  1. Broaden your search terms — try fewer keywords or remove date filters
  2. Check that the selected data sources (PubMed, BioRxiv, arXiv, etc.) are appropriate for your topic
  3. Try a different search mode (e.g., switch from "novelty-first" to "evidence-first")
  4. Verify your internet connection — literature search requires external API access
  5. For PubMed searches, ensure the NCBI API key is configured (contact your administrator)

Citation network graph is empty or incomplete

Symptoms

  • •Network canvas shows no nodes or edges
  • •Only a few papers appear when many were selected
  • •Community detection returns a single cluster
  • •Graph layout is overlapping or unreadable

Solutions

  1. Ensure you have selected at least 5-10 papers for meaningful network analysis
  2. Wait for the graph builder agent to finish processing — check the Run Console for progress
  3. Try papers with more citations/references for richer network connections
  4. Use the zoom and pan controls to navigate large graphs
  5. Papers without DOIs or reference metadata may not form edges — check the Work Inspector for details

Evidence extraction is slow or incomplete

Symptoms

  • •Evidence Matrix shows loading spinner for extended periods
  • •Some papers show "N/A" for PICO elements or outcomes
  • •Extraction quality varies across papers

Solutions

  1. Evidence extraction runs an AI agent per paper — larger batches take longer. Process 10-20 papers at a time
  2. Papers without full abstracts may yield incomplete extractions — check that abstracts were fetched
  3. Try re-running extraction for individual papers using the Work Inspector panel
  4. Ensure your subscription plan supports the required AI tier for evidence extraction

Literature-to-Chat bridge not working

Symptoms

  • •Send to Chat button does not respond
  • •Papers do not appear in the chat session
  • •Quick-action buttons (Summarize, Find conflicts) are missing

Solutions

  1. Ensure you have selected at least one paper before clicking Send to Chat
  2. Navigate to the Chat tab after sending — the literature packet appears as a new message
  3. Check that you have an active chat session in the project
  4. Try refreshing the page if the bridge fails to connect

Cannot log in or session expired

Symptoms

  • •Redirected to login page unexpectedly
  • •"Session expired" message
  • •Login button does not work
  • •Account shows "pending approval"

Solutions

  1. Clear cookies for this site and try logging in again
  2. Ensure your browser allows cookies
  3. If your account shows pending, contact your administrator for approval
  4. Check that your account is active with your administrator
  5. Try using an incognito/private browser window

Interview questions reappear after answering and navigating away

Symptoms

  • •Clarifying questions CATO asked are shown again after you answered them
  • •Questions reappear after switching conversations and returning
  • •Interview form shows even though analysis already completed

Solutions

  1. This was resolved in v1.2.2. Update to the latest version to get the fix
  2. If you see questions after answering them, submit blank answers to dismiss the form and allow the analysis to proceed with the answers already submitted
  3. If the issue persists after updating, start a new chat session for the same request
  4. Check that your browser is not caching an outdated version of the app (Ctrl/Cmd + Shift + R to hard-refresh)

Chat stream does not resume after navigating away and returning

Symptoms

  • •Returning to chat while CATO is generating shows a blank or frozen message
  • •Streaming indicator disappears but no response appears
  • •Response appears all at once with a long delay instead of streaming

Solutions

  1. CATO reconnects automatically to in-progress streams when you return. Wait 2-3 seconds for the reconnect to complete
  2. If streaming does not resume after 10 seconds, refresh the page. The completed response will load from the database
  3. Ensure you have a stable internet connection. Reconnect requires a live connection to the server
  4. If the reconnect indicator (cancel button and progress display) does not appear, try navigating away and back once more

Tour or welcome animation replaying after login

Symptoms

  • •Interactive tour appears again after you already completed or skipped it
  • •Welcome animation replays when logging in on a different device or browser
  • •Tour state seems to reset periodically

Solutions

  1. This is typically caused by a network error preventing the tour state from syncing to the server. CATO now retries the sync automatically up to 3 times
  2. Try completing or skipping the tour again — the state will be saved both locally and to the server with retry logic
  3. If the issue persists, clear your browser cache and local storage, then log in and complete the tour once more
  4. Ensure you have a stable internet connection when completing the tour, as the sync requires a successful server round-trip

AI features blocked or budget exceeded

Symptoms

  • •"Budget exceeded" or HTTP 403 error when sending chat messages
  • •Literature search refuses to run
  • •"Upgrade your plan" prompt appears unexpectedly

Solutions

  1. Check your current usage in Settings → Billing — usage is displayed as a percentage of your monthly AI budget
  2. Monthly budgets reset on the 1st of each month. Wait for the reset or upgrade your plan for a higher budget
  3. Free ($3/month), Base ($15/month), Pro ($80/month), Pay-as-you-go and Enterprise have unlimited budgets
  4. Contact your administrator if you believe the limit is incorrect

Study type filter returning unexpected results

Symptoms

  • •Filtering by "RCT" returns papers about data extraction or other unrelated topics
  • •Study type filter returns too few results
  • •Some study types (e.g., Cohort, Case-control) seem less effective than others

Solutions

  1. CATO uses word-boundary matching — "RCT" only matches the exact term, not substrings like "extraction". If you see false matches, refresh and try again
  2. For PubMed, study types like RCT, Meta-analysis, Systematic Review, and Review are filtered server-side using PubMed Publication Type tags. These are the most reliable
  3. Cohort and Case-control are filtered by text matching on abstracts and metadata, which may be less precise since PubMed does not have corresponding Publication Type tags
  4. Try combining study type filters with more specific search terms for better precision
  5. For comprehensive systematic reviews, use the Systematic Review feature (Pro tier and above) instead of manual study type filtering

Send to Chat not loading literature context

Symptoms

  • •Chat input appears to work but no literature packet is visible
  • •Quick-action buttons (Summarize, Find conflicts) are missing
  • •Chat input seems disabled or unresponsive after navigating from Literature

Solutions

  1. Wait for the literature packet to fully load — the chat input is temporarily disabled while the packet downloads
  2. If the packet fails to load, try navigating back to Literature Intelligence and clicking "Send to Chat" again
  3. Check your internet connection — the packet requires a round-trip to the server
  4. Starting a New Chat clears any loaded literature context. If you need the context, do not start a new chat before sending your message
  5. Try refreshing the page if the issue persists

Figure editor not loading or shows "No SVG available"

Symptoms

  • •Clicking the edit (pencil) icon shows a blank editor
  • •Editor displays "No SVG available" message
  • •Figure elements cannot be selected in the editor

Solutions

  1. The figure editor requires SVG data generated alongside the PNG. If the figure was created before the editor feature was available, the SVG may not exist. Try regenerating the figure by re-running the analysis
  2. Ensure the figure is not a 3D molecular structure (3Dmol.js). 3D structures use WebGL and cannot be edited in the SVG editor
  3. If elements cannot be selected, they may be classified as background or grid elements. Only data elements, labels, legends, and annotations are selectable by design
  4. Try refreshing the page and reopening the editor
  5. The Figure Editor requires Base plan or above. Free-tier users see a locked overlay
  6. If the issue persists, submit a support ticket with the conversation ID and figure name

3D molecular viewer shows loading spinner indefinitely

Symptoms

  • •Loading spinner appears but never resolves to a 3D structure
  • •3D molecular model does not appear after requesting a structure
  • •Viewer area remains blank with "Loading structure data..." message

Solutions

  1. Large PDB structures (>32KB) are streamed in chunks and may take a few seconds to assemble. Wait for the loading indicator to complete
  2. Verify the PDB ID or structure data is valid. Try a known structure like "PDB 1CRN" to confirm the viewer works
  3. Check your network connection. Chunked data requires a stable connection to assemble correctly
  4. Try refreshing the page. If the stream was interrupted mid-transfer, a refresh will re-fetch the data
  5. Ensure you are on a Base plan or above. The 3D molecular viewer is a premium feature
  6. If the issue persists, try a different browser (Chrome recommended) and submit a support ticket

Still Having Issues?

If none of the above solutions resolve your problem, please contact support with the following information:

  • Description of the issue
  • Steps to reproduce
  • Browser and operating system
  • Any error messages