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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter #502

Open jjjjjj17 opened 1 month ago

jjjjjj17 commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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