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No decoys found in the FASTA file? #1675
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Could you share your workflow file! Thanks, Fengchao |
Yes, here it is: fragpipe-220.workflow.zip |
You should change the decoy tag to database.decoy-tag=rev_ Best, Fengchao |
@fcyu I reopen the issue because after running the fragpipe I got some unexpected messages and stopped before ending properly. I think that the problem is that it cannot run PeptideProphet:
I searched for a similar error in the issues and I found this one: That was related with precisely the decoy sequences but I think that in my case they are OK...Any idea? This is my log: fragpipe22_manual_decoy.log.zip Thanks! |
The warnings you found won't affect the results. The crash was because the PeptideProphet models failed, and then there was no IDs. If you are doing a closed search, why not using Percolator? Iterations: .........10.........20....WARNING: Mixture model quality test failed for charge (1 ).
.
WARNING: Mixture model quality test failed for charge (2 ).
WARNING: Mixture model quality test failed for charge (3 ).
WARNING: Mixture model quality test failed for charge (4 ).
WARNING: Mixture model quality test failed for charge (5 ).
WARNING: Mixture model quality test failed for charge (6 ).
WARNING: Mixture model quality test failed for charge (7 ). Best, Fengchao |
Ok, I see. Do you mean |
You still have PeptideProphet running peptide-prophet.run-peptide-prophet=true
percolator.run-percolator=false Best, Fengchao |
Hello
I formatted a Human FASTA file using my own scripts for creating the decoy and Philosopher but I get from FragPipe this error:
2024-07-16 11:01:27,686 ERROR - No decoys found in the FASTA file.
I reviewed the FASTA and it seems OK and following the guidelines seen at the Philospher doc. Do you know why this error?
Thanks!
The file: sp_human_decoy_cont_formatted.fasta.zip
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