Table of contents

  1. Troubleshooting basics
  2. Configuration
  3. Input and output errors
  4. Early crash
  5. Stuck on revision
  6. Crash halfway through
  7. Pipeline update doesn’t work
  8. Unable to acquire lock error
  9. Docker permission errors

How to use these pages

  1. Search your specific error message in the website search bar (shortcut ctrl+k)
  2. Read the titles of each section to see if the error appears to match your error
  3. Follow the troubleshooting basics, to
    • to try to reproduce the error
    • to inspect more places to gather information regarding the problem
  4. If you can’t find your error message here, or a solution to your problem, fails, please ask for help
Bytesize talk

There is a Bytesize talk by Phil Ewels on the topic of troubleshooting, which you may find useful. See also the accompanying slides.

Extra resources and getting help

If you still have an issue with running the pipeline then feel free to contact us via Slack or by opening an issue in the respective pipeline repository on GitHub asking for help.


If you have problems that are directly related to Nextflow and not nf-core then please visit the Nextflow community forum.