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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
109 stars 17 forks source link

Philosopher: Cannot read file. Error parsing the file. #485

Open WenSheng-Ye opened 4 months ago

WenSheng-Ye commented 4 months ago

Hi, I have discovered a bug with Philosopher. Console Information: INFO[21:32:23] Executing Filter v5.1.0
INFO[21:32:23] Processing peptide identification files
INFO[21:32:23] Parsing G:\WSY\Output_LC2_20240222\LC2_HILIC\interact.mod.pep.xml ERRO[21:32:23] Cannot read file. Error parsing the file
Process 'PhilosopherFilter' finished, exit code: 1 Process returned non-zero exit code, stopping

Log File: log_2024-02-22_21-32-23.txt

Hope that I can get your help.

Yours, Sheng-Ye

hsiaoyi0504 commented 4 months ago

It's weird that there is an error: command "chmod 664 interact.mod.pep.xml" failed: Operation not permitted Do you see the file there? What's the file permission you see?

WenSheng-Ye commented 4 months ago

interact.mod.pep.xml.zip I have Uploaded the file, hope that can be useful.

Patrick-L-White commented 2 months ago

Did you end up solving this issue? I am having the same one...

hsiaoyi0504 commented 2 months ago

@Patrick-W1345 Your issue #492 seems to be different. This one showed an error message regarding the file permission.