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Issues list

ProteinProphet Error help wanted Extra attention is needed
#261 opened Aug 13, 2021 by uonnet updated Apr 13, 2023
@prvst
14
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 updated Jul 4, 2023
1
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 updated Jul 4, 2023
FDR ISSUE
#464 opened Sep 22, 2023 by kwynne71 updated Sep 27, 2023
2
Format error in combined_protein.tsv when MS1 quant is disabled
#474 opened Nov 14, 2023 by hollenstein updated Nov 22, 2023
1
Missing protein coverage column
#486 opened Feb 23, 2024 by lyons89 updated Feb 23, 2024
Failed Mass offset search for PAL (without PTMProphet): PeptideProphet Error Message
#487 opened Mar 2, 2024 by chaudngo updated Mar 2, 2024
protein start and end positions not showing in combined peptides report.
#480 opened Dec 15, 2023 by heuselm updated Mar 9, 2024
1
Philosopher: Cannot read file. Error parsing the file.
#485 opened Feb 22, 2024 by WenSheng-Ye updated May 7, 2024
4
Philosopher crashes with large pep.xml
#494 opened May 27, 2024 by BernhardRetzl updated May 27, 2024
Help with understanding where files are written during the creation of combined.prot.xml
#495 opened Jun 3, 2024 by Patrick-L-White updated Jun 3, 2024
troubles with generating Philosopher report .meta/pep.bin
#496 opened Jun 4, 2024 by nissrine895 updated Jun 4, 2024
Process 'PhilosopherFilter' finished, exit code: 2
#499 opened Mar 4, 2023 by jmcalist updated Jul 16, 2024
@prvst
12
Fix or remove the warning from ProteinProphet: WARNING: Found the following zero-mass residues in protein entry ***
#501 opened Jul 25, 2024 by fcyu updated Jul 25, 2024
@guoci @fcyu
'mv' is not recognized as an internal or external command, operable program or batch file.
#497 opened Jun 21, 2024 by weaversd updated Aug 1, 2024
1
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 updated Oct 1, 2024
5
protein FDR filter didn't reach the desired threshold error
#503 opened Aug 29, 2024 by mozzaLB updated Oct 14, 2024
7
Filter command: panic: Cannot write file. cannot create protein report
#506 opened Oct 14, 2024 by hcadre updated Oct 15, 2024
4
PProcess 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping
#507 opened Oct 25, 2024 by baynec2 updated Oct 25, 2024
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 updated Nov 20, 2024
No peptides and spectral but identified as a protein
#513 opened Nov 22, 2024 by LiTing99-cutie updated Nov 23, 2024
@fcyu
3
Database - cannot download redundant proteomes or in-house - java.lang error
#514 opened Nov 30, 2024 by Althalis updated Nov 30, 2024
1
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 updated Dec 13, 2024
5
Incorrect Extended Peptide in `psm.tsv
#518 opened Dec 19, 2024 by fcyu updated Dec 19, 2024
Non-zero exit code MS Fragger
#519 opened Jan 9, 2025 by talithar-star updated Jan 9, 2025
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