Hi there-- I am trying out this "Start from: DIA Raw" option during Import Peptide Search of our DIA results. It runs for several hours but then gets an error message. Here is how it ends:
"[2024/02/21 12:08:14] INFO: Issued command:
[2024/02/21 12:08:14] INFO: percolator --results-peptides D:\dia_mzml\231101_dia_mzml_rename\crux-output/percolator.target.peptides.txt --decoy-results-peptides D:\dia_mzml\231101_dia_mzml_rename\crux-output/percolator.decoy.peptides.txt --results-psms D:\dia_mzml\231101_dia_mzml_rename\crux-output/percolator.target.psms.txt --decoy-results-psms D:\dia_mzml\231101_dia_mzml_rename\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc D:\dia_mzml\231117_dia_mzml_rename\0006-231116-A1-INA-diaumpire.fixed.pin
[2024/02/21 12:08:14] INFO: Started Wed Feb 21 12:08:14 2024
[2024/02/21 12:08:14] INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
[2024/02/21 12:08:14] INFO: Reading tab-delimited input from datafile D:\dia_mzml\231117_dia_mzml_rename\0006-231116-A1-INA-diaumpire.fixed.pin
[2024/02/21 12:08:14] INFO: Features:
[2024/02/21 12:08:14] INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7
[2024/02/21 12:08:14] INFO: Found 28 PSMs
[2024/02/21 12:08:14] INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
[2024/02/21 12:08:14] INFO: Train/test set contains 28 positives and 0 negatives, size ratio=inf and pi0=1
[2024/02/21 12:08:14] FATAL: An exception occurred: Error: no decoy PSMs were provided.
[2024/02/21 12:08:14]
[2024/02/21 14:20:21] Search canceled."
The full output is attached as well as a pdf of my settings. I can provide the mzML files and the fasta.
Thanks
Bill