Scaffold Error: Percolator Exited with Non-zero Status

Occasionally when running Scaffold (or any tool that users Percolator), users may encounter the following Percolator related error message.


This error occurs whenever Percolator fails to run successfully. It can be interpreted as no peptides pass the peptide level FDR threshold that was set when data was loaded. Raising the peptide level FDR threshold is often a way to gain a better understanding of this error. However, a more comprehensive analysis is needed:

  • This message occurs whenever percolator fails to run successfully
  • Typically this is when it's not possible to reach the target peptide FDR
  • It can occur for other reasons, you have to check the logs

Note, in order to change the peptide level FDR the data must be reloaded into Scaffold DIA. This parameter can be found on the Search tab of the Load Data workflow dialog. Additionally, using a different library may prevent this error from occurring. If these suggestions do not solve the issue, a deeper dive in to the data or the experimental design may be necessary.

The first step is to send us your error and output logs, found by going to Help > Show Log Files. Send these to use by opening a ticket in our Help Center.

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