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

[jjjjjj17]

Hello!! I have a problem running my data, can you help me find out why?
Here is the log file
log_2024-07-29_23-45-15.txt

[dpolasky]

From the log:
time="23:45:15" level=error msg="the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter"

It looks like you have millions of "proteins" in your fasta file, and it was not possible to filter the results to achieve a 1% protein level FDR. You can try setting a higher protein FDR threshold as suggested. It is an unusual fasta file, so your search may need special handling - but it's hard to say without knowing more about your search and data.

Best,
Dan

[fcyu]

I saw similar errors several times before, and it seems to be a Philosopher bug. I always wanted to test or let someone take a look at this bug. Let me transfer it to Philosopher repository to keep track of it easier.

Best,

Fengchao

[liorlobel]

Dear Fengchao,

I also get this error with my data. It is a DIA-speclib workflow run.

time="16:20:04" level=info msg="1+ Charge profile" decoy=126 target=2918 time="16:20:04" level=info msg="2+ Charge profile" decoy=841 target=128944 time="16:20:04" level=info msg="3+ Charge profile" decoy=416 target=53296 time="16:20:04" level=info msg="4+ Charge profile" decoy=84 target=7524 time="16:20:04" level=info msg="5+ Charge profile" decoy=34 target=514 time="16:20:04" level=info msg="6+ Charge profile" decoy=0 target=0 time="16:20:05" level=info msg="Database search results" ions=30379 peptides=21709 psms=194697 time="16:20:05" level=info msg="Converged to 0.78 % FDR with 193196 PSMs" decoy=1501 threshold=0.700198 total=194697 time="16:20:05" level=info msg="Converged to 0.99 % FDR with 17895 Peptides" decoy=178 threshold=0.995283 total=18073 time="16:20:05" level=info msg="Converged to 1.00 % FDR with 26821 Ions" decoy=268 threshold=0.984225 total=27089 time="16:20:05" level=info msg="Protein inference results" decoy=925 target=2409 time="16:20:05" level=error msg="the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter" panic: the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter

Could it be because some of my samples (25 overall, 24 DIA, and 1 DDA for spec library generation) have low identifications? But most samples have decent identifications. I'm not expecting too many because these are immunoprecipitation samples.

Any ideas?

I attach the filter.log file.

Thanks,

Lior

filter.log

[liorlobel]

I can provide mzML files, if needed.

[AimeeD90]

yes please, and it would be more helpful if you can directly provide the .pep.xml files with this error.