Katalyst: Slow or stuck ReprocessExperiment tasks

Description

• Users run ReprocessExperiment for large or complex experiments and observe:
  • Very long reprocessing times.
  • Tasks that appear stuck or never complete.
• Katalyst may become sluggish during these operations, affecting other users.

Solution

• Check server resources during reprocessing:
  • CPU, memory, and disk I/O usage.
  • If the server is saturated, reprocessing might be contending with other workloads.
• Review processing templates:
  • Complex or overly aggressive processing (e.g., many traces, heavy deconvolution) can significantly increase runtime.
  • Simplify templates where possible, or split processing into steps.
• Use scheduling and throttling:
  • Run heavy reprocessing tasks during off‑peak hours.
  • Limit the number of concurrent reprocessing jobs if your environment supports it.
• Inspect logs:
  • Look for repeated warnings or errors in ReprocessExperiment logs, which may indicate a loop or a problematic plate/well. Navigate to the Common Logs directory. The path is defined in the CONFIG.INI file under:
    [Paths]: CommonLogsDir.
  • If a specific experiment always hangs, isolate it and test in a lower environment.