PhilosopherFilter error

[jongminchoi]

log_2025-10-09_21-38-17.txt

Hello,
I used a customized DB to search some isoforms.
During PSM validation I met an error and couldn't solve.
And do not know what exact problem is.
Please help me to solve it.

Thank you.

[jongminchoi]

Any chance to look at my problem? I still cannot not solve it. Could you please help to solve the issue?

[AimeeD90]

@jongminchoi This crash is typically seen when searching a customized database, and it has been fixed recently. Please try with this new version https://www.dropbox.com/scl/fo/wi9u900jdw08vhkh5zqe0/APvIfPw1koglO-jRICad2U4?rlkey=xk2nmpf09u6ox0vsc7pe9pdie&st=9hrv23tv&dl=0.

[jongminchoi]

Thank you!
Can I just download .exe file and install it? I could not find the update button in Fragpipe itself.
Great appreciate!

[jongminchoi]

I have changed the file in the philosopher folder and ran again.
Looks version was updated but still got the error as below.
Could you please look at it?

Thank you!!

PhilosopherFilter [Work dir: C:\Users\hygen\Documents\HLA_4digits_10302025_2\F_MPM152_2_Lat_IPept_HLA_ABC_Protein_half]
C:\FragPipe\FragPipe-23.1\tools\Philosopher\philosopher-v5.1.3.exe filter --sequential --prot 0.01 --picked --tag rev_ --pepxml C:\Users\hygen\Documents\HLA_4digits_10302025_2\F_MPM152_2_Lat_IPept_HLA_ABC_Protein_half --protxml C:\Users\hygen\Documents\HLA_4digits_10302025_2\combined.prot.xml --razor
time="13:22:45" level=info msg="Executing Filter v5.1.3"
time="13:22:45" level=info msg="Processing peptide identification files"
time="13:22:45" level=info msg="Parsing C:\Users\hygen\Documents\HLA_4digits_10302025_2\F_MPM152_2_Lat_IPept_HLA_ABC_Protein_half\interact-F_MPM152_2_Lat_IPept_HLA_ABC_Protein_half.pep.xml"
time="13:23:41" level=info msg="1+ Charge profile" decoy=0 target=0
time="13:23:41" level=info msg="2+ Charge profile" decoy=45 target=517
time="13:23:41" level=info msg="3+ Charge profile" decoy=20 target=260
time="13:23:41" level=info msg="4+ Charge profile" decoy=16 target=55
time="13:23:41" level=info msg="5+ Charge profile" decoy=3 target=10
time="13:23:41" level=info msg="6+ Charge profile" decoy=2 target=9
time="13:23:41" level=info msg="Database search results" ions=448 peptides=386 psms=937
time="13:23:41" level=info msg="Converged to 0.98 % FDR with 613 PSMs" decoy=6 threshold=0.789074 total=619
time="13:23:41" level=info msg="Converged to 0.65 % FDR with 155 Peptides" decoy=1 threshold=0.858267 total=156
time="13:23:41" level=info msg="Converged to 0.97 % FDR with 206 Ions" decoy=2 threshold=0.83324 total=208
time="13:23:41" level=info msg="Protein inference results" decoy=1 target=1847
time="13:23:41" level=info msg="Converged to 0.39 % FDR with 257 Proteins" decoy=1 threshold=0.5 total=258
time="13:23:42" level=info msg="Applying sequential FDR estimation" ions=223 peptides=180 psms=619
time="13:23:42" level=info msg="613 PSMs" decoy=5 threshold=0.78991 total=618
time="13:23:42" level=info msg="155 Peptides" decoy=1 threshold=0.858267 total=156
time="13:23:42" level=info msg="206 Ions" decoy=2 threshold=0.83324 total=208
time="13:23:42" level=info msg="Post processing identifications"
time="13:23:42" level=info msg="Assigning protein identifications to layers"
Error: B35319 is not in the database
Process 'PhilosopherFilter' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 8 remaining tasks