Katalyst: Data processing failed and files were moved to the Failed folder

Description
Raw data intended for processing is moved into the Failed Files Location (Instrument Parameters → Failed Files Location) when automated processing fails.

To diagnose the issue, review both:

• Automation Server Scripts log files, and
• Health Checker log files, which contain root-cause error messages.

Solution

Validate upload target & experiment setup

• Confirm data is uploaded to a valid Analysis container
• Confirm the experiment has been saved before data is uploaded and processed.

Validate file-level requirements

• Confirm correct naming of files.
• Confirm Scan Mask is correct for the specific instrument and matches the data type/format being uploaded.
• Confirm files are not compressed/zipped (unless your workflow explicitly supports zipped uploads and the appropriate configuration is set).

Handle Empower-specific conflict (if applicable)

If Empower analytical data is being uploaded to a container that already contains analytical data:

• Remove the relevant documents from MongoDB in the empower_imported_ids collection for that container and project, corresponding to the relevant injection IDs.

Review logs to locate the root cause

• Automation Server (processing) logs
  • Open the Common Logs directory (from CONFIG.INI → [Paths] → CommonLogsDir).
  • In the dated subfolder, open the log file for the relevant process and review for errors.
• Health Checker logs
  • Open the folder containing Health Checker logs (from CONFIG.INI → [Paths] → HealthCheckerLogsDir).
  • Open mainHealthChecker.fsbin and search for error messages.

What Health Checker validates:

• The accuracy of paths defined in the Instruments and KAT_Sequence record sets, and
• Connectivity between system components.