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PhilosopherFilter crash - error parsing file #563

@EllenBoswell

Description

@EllenBoswell

- 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.)

log_2026-04-21_13-11-52.zip

- Describe the issue or question:
Hello,
I am using FragPipe 24.0 (headless) with an open search workflow file. When analysing multiple files together, FragPipe seems to crash at the PhilosopherFilter step (please see the log):

time="14:11:52" level=error msg="Cannot read file. Error parsing the file "
Process 'PhilosopherFilter' finished, exit code: 1

However, if I split the files up and run FragPipe separately on each, it works well. Can anybody help with what might be causing this error please? I have used FragPipe on other data sets without any crashes.
Thanks,
Ellen

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