Issues

• Philosopher 'filter' crashes with 'fatal error: runtime: out of memory' on large metaproteomic database (2.5M proteins, 83 mzML files)

  Nesvilab/philosopher#565 · Filter by author martinastramacci opened on Jul 29, 2026
  2

• Unable to compile Philosopher : undefined: Asset

  Nesvilab/philosopher#564 · Filter by author jmk-3bio opened on Jul 22, 2026

• PhilosopherFilter crash - error parsing file

  Nesvilab/philosopher#563 · Filter by author EllenBoswell opened on Apr 21, 2026

• "Error: peptide [x] was assigned to [protein y] that is not the database"

  Nesvilab/philosopher#558 · Filter by author a-indra opened on Feb 6, 2026
  4

• Spectral library generation using FragPipe 23.1: Process 'PhilosopherFilter' finished, exit code: 137

  Nesvilab/philosopher#557 · Filter by author andrewyy677 opened on Jan 25, 2026
  1

  

• Missing libz so file

  Nesvilab/philosopher#554 · Filter by author bernt-matthias opened on Dec 17, 2025
  5

• Philosopher filter: time="11:59:11" level=error msg="Cannot read file. Error parsing the file "

  Nesvilab/philosopher#552 · Filter by author rjvortega opened on Dec 10, 2025

• Cannot read file. Error parsing, exit code: 1

  Nesvilab/philosopher#547 · Filter by author winnieWei123456 opened on Oct 27, 2025
  2

• Where is the output database?

  Nesvilab/philosopher#545 · Filter by author thh32 opened on Oct 13, 2025

• PhilosopherFilter error

  Nesvilab/philosopher#544 · Filter by author jongminchoi opened on Oct 10, 2025
  4

  

• variation in open-search results

  Nesvilab/philosopher#542 · Filter by author animesh opened on Sep 2, 2025
  7

  

• The execution of the Philosopher was unexpectedly stuck.

  Nesvilab/philosopher#541 · Filter by author huangcx1539 opened on Aug 30, 2025

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

  Nesvilab/philosopher#540 · Filter by author alessandro-vai opened on Aug 21, 2025
  2

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

  Nesvilab/philosopher#539 · Filter by author marlenejarap opened on Aug 5, 2025
  2

• Error when running a non-standard database (antibodies)

  Nesvilab/philosopher#538 · Filter by author yishai99 opened on Jul 29, 2025
  1

• : 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"

  Nesvilab/philosopher#537 · Filter by author LGFANGA opened on Jul 22, 2025
  1

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

  Nesvilab/philosopher#534 · Filter by author hruskamiro opened on Jun 5, 2025

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

  Nesvilab/philosopher#531 · Filter by author 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

  Nesvilab/philosopher#528 · Filter by author hupak2022 opened on Apr 1, 2025
  2

• error: Cannot deploy asset. InteractParser.

  Nesvilab/philosopher#527 · Filter by author yashacode opened on Mar 28, 2025

• Fragpipe protein prophet crash

  Nesvilab/philosopher#524 · Filter by author NikolaMonteverde opened on Mar 17, 2025

• Inflation in peptide IDs after group specific FDR

  Nesvilab/philosopher#522 · Filter by author mkirankumar45 opened on Feb 10, 2025
  7

• combined_protein.tsv with empty sample columns

  Nesvilab/philosopher#520 · Filter by author loganjohnson0 opened on Jan 25, 2025
  4

  

• Non-zero exit code MS Fragger

  Nesvilab/philosopher#519 · Filter by author talithar-star opened on Jan 9, 2025

• Incorrect Extended Peptide in `psm.tsv

  Nesvilab/philosopher#518 · Filter by author fcyu opened on Dec 19, 2024