: iostream error time="12:44:06" level=error msg="Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files"

[LGFANGA]

- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question:

log_2025-07-22_12-44-06.txt

Dear friend,​
I am using FragPipe for the quantitative analysis of TIMS TOF-PASEF DDA data. However, an error persists: "iostream error time="12:44:06" level=error msg="Cannot execute program. There was an error with ProteinProphet; please check your parameters and input files". I am at a loss and have to turn to you for help.

[AimeeD90]

It's difficult for us to tell what caused the ProteinProphet crash, but looks like it might be related to the input pep.xml files, please rerun the search using a random subset of raw files to see if the crash still occurs. If you can locate which run caused the crash, I will then take a look at that pep.xml file to figure it out