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26 Open 305 Closed
26 Open 305 Closed
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Issues list

Incorrect Extended Peptide in `psm.tsv
#518 opened Dec 19, 2024 by fcyu
Adding the contam_ prefix doesn't work with an existing database. It only works when downloading the database using Philosopher
#516 opened Dec 13, 2024 by lxavierneves
5
Database - cannot download redundant proteomes or in-house - java.lang error
#514 opened Nov 30, 2024 by Althalis
1
No peptides and spectral but identified as a protein
#513 opened Nov 22, 2024 by LiTing99-cutie
@fcyu
3
panic: the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter
#511 opened Nov 20, 2024 by FloorWur
--decoys doesn't work for the DIA data
#512 opened Nov 19, 2024 by nitz1bug
1
PProcess 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping
#507 opened Oct 25, 2024 by baynec2
Filter command: panic: Cannot write file. cannot create protein report
#506 opened Oct 14, 2024 by hcadre
4
protein FDR filter didn't reach the desired threshold error
#503 opened Aug 29, 2024 by mozzaLB
7
the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter
#502 opened Jul 30, 2024 by jjjjjj17
5
Fix or remove the warning from ProteinProphet: WARNING: Found the following zero-mass residues in protein entry ***
#501 opened Jul 25, 2024 by fcyu
@guoci @fcyu
'mv' is not recognized as an internal or external command, operable program or batch file.
#497 opened Jun 21, 2024 by weaversd
1
troubles with generating Philosopher report .meta/pep.bin
#496 opened Jun 4, 2024 by nissrine895
Help with understanding where files are written during the creation of combined.prot.xml
#495 opened Jun 3, 2024 by Patrick-L-White
Philosopher crashes with large pep.xml
#494 opened May 27, 2024 by BernhardRetzl
ERRO[11:53:33] the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter
#493 opened May 14, 2024 by Luc2702
Failed Mass offset search for PAL (without PTMProphet): PeptideProphet Error Message
#487 opened Mar 2, 2024 by chaudngo
Missing protein coverage column
#486 opened Feb 23, 2024 by lyons89
Philosopher: Cannot read file. Error parsing the file.
#485 opened Feb 22, 2024 by WenSheng-Ye
4
protein start and end positions not showing in combined peptides report.
#480 opened Dec 15, 2023 by heuselm
1
Format error in combined_protein.tsv when MS1 quant is disabled
#474 opened Nov 14, 2023 by hollenstein
1
FDR ISSUE
#464 opened Sep 22, 2023 by kwynne71
2
Process 'PhilosopherFilter' finished, exit code: 2
#499 opened Mar 4, 2023 by jmcalist
@prvst
12
Feature request: Add Indistinguishable Proteins column also to psm, ion and peptide tables enhancement New feature or request
#448 opened Aug 3, 2022 by hollenstein
Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.
#447 opened Dec 16, 2021 by fcyu
1
ProTip! Adding no:label will show everything without a label.