INFO: CPU: calc-server INFO: Crux version: 3.1-f2e7488 INFO: Tue Jun 19 18:07:59 MSK 2018 COMMAND LINE: /home/mark/crux/bin/crux percolator /home/mark/overfit_test/comet/confetti_trypsin_01_3.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet_proteins --fileroot confetti_trypsin_01_3 --protein T --overwrite T --fido-empirical-protein-q T --protein-report-duplicates T INFO: Beginning percolator. INFO: Reading file /home/mark/overfit_test/comet/confetti_trypsin_01_3.comet.target.pep.xml ERROR: Decoy file '/home/mark/overfit_test/comet/confetti_trypsin_01_3.comet.decoy.pep.xml' doesn't exist INFO: Converting input to pin format. INFO: Parsing /home/mark/overfit_test/comet/confetti_trypsin_01_3.comet.target.pep.xml INFO: Assigning index 0 to /home/mark/overfit_test/comet/confetti_trypsin_01_3.comet.target.pep.xml. INFO: There are 41061 target matches and 9632 decoys INFO: Maximum observed charge is 6. INFO: File conversion complete. INFO: Percolator version 3.02.0, Build Date Mar 21 2018 17:24:57 INFO: Copyright (c) 2006-9 University of Washington. All rights reserved. INFO: Written by Lukas Käll (lukall@u.washington.edu) in the INFO: Department of Genome Sciences at the University of Washington. INFO: Issued command: INFO: percolator --results-peptides /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.01 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --protein-report-duplicates --fido-protein --fido-empirical-protein-q --fido-gridsearch-depth 0 --fido-fast-gridsearch 0 --fido-protein-truncation-threshold 0.01 --fido-gridsearch-mse-threshold 0.05 --results-proteins /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.target.proteins.txt --decoy-results-proteins /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.percolator.decoy.proteins.txt --post-processing-tdc /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.make-pin.pin INFO: Started Tue Jun 19 18:08:02 2018 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_3.make-pin.pin INFO: Features: INFO: lnrSp XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 enzN enzC enzInt lnNumDSP dM absdM INFO: Found 50693 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 41061 positives and 9632 negatives, size ratio=4.26298 and pi0=1 INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 2 as initial direction. Could separate 17760 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 2 as initial direction. Could separate 17508 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 2 as initial direction. Could separate 17611 training set positives with q<0.01 in that direction. INFO: Found 26396 test set positives with q<0.01 in initial direction INFO: Reading in data and feature calculation took 2.40904 cpu seconds or 2 seconds wall clock time. INFO: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 INFO: Iteration 1: Estimated 29330 PSMs with q<0.01 INFO: Iteration 2: Estimated 29979 PSMs with q<0.01 INFO: Iteration 3: Estimated 30077 PSMs with q<0.01 INFO: Iteration 4: Estimated 30081 PSMs with q<0.01 INFO: Iteration 5: Estimated 30093 PSMs with q<0.01 INFO: Iteration 6: Estimated 30101 PSMs with q<0.01 INFO: Iteration 7: Estimated 30112 PSMs with q<0.01 INFO: Iteration 8: Estimated 30121 PSMs with q<0.01 INFO: Iteration 9: Estimated 30109 PSMs with q<0.01 INFO: Iteration 10: Estimated 30118 PSMs with q<0.01 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -1.6115 -1.2967 -1.6296 lnrSp INFO: 2.7878 2.9378 3.1320 XCorr INFO: -0.1443 -0.2468 -0.2680 Sp INFO: 0.1846 0.3325 0.1856 IonFrac INFO: -0.3925 -0.2604 -0.4555 PepLen INFO: 0.0000 0.0000 0.0000 Charge1 INFO: -0.0430 -0.0171 0.0070 Charge2 INFO: 0.0228 -0.0006 -0.0444 Charge3 INFO: 0.0305 0.0125 0.0591 Charge4 INFO: 0.0400 0.0647 0.0405 Charge5 INFO: 0.0057 0.0748 0.0411 Charge6 INFO: 0.0000 0.0000 0.0000 enzN INFO: 0.0000 0.0000 0.0000 enzC INFO: -0.4883 -0.4898 -0.4826 enzInt INFO: -0.0598 -0.1077 -0.1103 lnNumDSP INFO: 0.2956 0.2970 0.3217 dM INFO: -0.1731 -0.2127 -0.1878 absdM INFO: 0.0075 0.2078 0.0065 m0 INFO: Found 30023 test set PSMs with q<0.01. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 41061 target PSMs and 9632 decoy PSMs. INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. INFO: Calculating q values. INFO: Final list yields 22056 target peptides with q<0.01. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 73.97 cpu seconds or 42 seconds wall clock time. INFO: INFO: Calculating protein level probabilities. INFO: Copyright (c) 2008-9 University of Washington. All rights reserved. INFO: Written by Oliver R. Serang (orserang@u.washington.edu) in the INFO: Department of Genome Sciences at the University of Washington. INFO: INFO: Initialized protein inference engine. INFO: Computing protein probabilities. INFO: The parameters for the model will be estimated by grid search. INFO: INFO: Estimating the parameters took : 3.70289 cpu seconds or 3 seconds wall time INFO: The following parameters have been chosen: INFO: alpha = 0.008 INFO: beta = 0.001 INFO: gamma = 0.5 INFO: INFO: Protein level probabilities will now be estimated INFO: Computing protein statistics. INFO: protein pi0 estimate = 0.7500742438 INFO: Number of protein groups identified at q-value = 0.01: 3717 INFO: Estimating protein probabilities took : 19.82 cpu seconds or 20 seconds wall clock time. INFO: Elapsed time: 68.4 s INFO: Finished crux percolator. INFO: Return Code:0