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Cannot read file. Error parsing, exit code: 1

Status: Open.

#547 In Nesvilab/philosopher;

· winnieWei123456 opened on Oct 27, 2025

Where is the output database?

Status: Open.

#545 In Nesvilab/philosopher;

· thh32 opened on Oct 13, 2025

PhilosopherFilter error

Status: Open.

#544 In Nesvilab/philosopher;

· jongminchoi opened on Oct 10, 2025

variation in open-search results

Status: Open.

#542 In Nesvilab/philosopher;

· animesh opened on Sep 2, 2025

The execution of the Philosopher was unexpectedly stuck.

Status: Open.

#541 In Nesvilab/philosopher;

· huangcx1539 opened on Aug 30, 2025

Error on 'Assigning protein identifications to layers' with group FDR

Status: Open.

#540 In Nesvilab/philosopher;

· alessandro-vai opened on Aug 21, 2025

Philosopher Protein ID and Gene in combined_proteins.tsv shows the full protein header

Status: Open.

#539 In Nesvilab/philosopher;

· marlenejarap opened on Aug 5, 2025

Error when running a non-standard database (antibodies)

Status: Open.

#538 In Nesvilab/philosopher;

· yishai99 opened on Jul 29, 2025

: 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"

Status: Open.

#537 In Nesvilab/philosopher;

· LGFANGA opened on Jul 22, 2025

Potentially Misleading Error Message When Input File Is Missing (philosopher filter)

Status: Open.

#534 In Nesvilab/philosopher;

· hruskamiro opened on Jun 5, 2025

"the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter"

Status: Open.

#531 In Nesvilab/philosopher;

· FelipeClement opened on May 23, 2025

Adding the contam_ prefix doesn't work with an existing database. It only works when downloading the database using Philosopher

Status: Open.

#528 In Nesvilab/philosopher;

· hupak2022 opened on Apr 1, 2025