No decoys found in the FASTA file?

[rolivella]

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

[fcyu]

Could you share your workflow file!

Thanks,

Fengchao

[rolivella]

Yes, here it is: fragpipe-220.workflow.zip

[fcyu]

You should change the decoy tag to database.decoy-tag=DECOY_:

database.decoy-tag=rev_

Best,

Fengchao

[rolivella]

@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:

time="15:54:08" level=info msg="Executing PeptideProphet  v5.1.1"
Unknown file type. No file loaded./home/proteomics/mygit/atlas-runs/520c5201-cc4e-4e32-a566-8504c41c27cc/59/571dd10648593fae17bab5703e7f3c/output/1_1/2024MQ024_MSGA_052_01_25pto.raw
Unknown file type. No file loaded./home/proteomics/mygit/atlas-runs/520c5201-cc4e-4e32-a566-8504c41c27cc/59/571dd10648593fae17bab5703e7f3c/output/1_1/2024MQ024_MSGA_052_01_25pto.raw

I searched for a similar error in the issues and I found this one:

https://github.com/Nesvilab/FragPipe/issues/1556

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!

[fcyu]

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

[rolivella]

Ok, I see. Do you mean percolator.run-percolator=true? I did it and got the same error log: fragpipe22_manual_decoy_v2.log.zip

[fcyu]

You still have PeptideProphet running

peptide-prophet.run-peptide-prophet=true
percolator.run-percolator=false

Best,

Fengchao