INFO: CPU: calc-server INFO: Crux version: 3.1-f2e7488 INFO: Tue Jun 19 18:17:01 MSK 2018 COMMAND LINE: /home/mark/crux/bin/crux percolator /home/mark/overfit_test/comet/confetti_trypsin_01_4.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet_proteins --fileroot confetti_trypsin_01_4 --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_4.comet.target.pep.xml ERROR: Decoy file '/home/mark/overfit_test/comet/confetti_trypsin_01_4.comet.decoy.pep.xml' doesn't exist INFO: Converting input to pin format. INFO: Parsing /home/mark/overfit_test/comet/confetti_trypsin_01_4.comet.target.pep.xml INFO: Assigning index 0 to /home/mark/overfit_test/comet/confetti_trypsin_01_4.comet.target.pep.xml. INFO: There are 40850 target matches and 9845 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_4.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_4.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_4.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_4.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_4.percolator.target.proteins.txt --decoy-results-proteins /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_4.percolator.decoy.proteins.txt --post-processing-tdc /home/mark/overfit_test/percolator_comet_proteins/confetti_trypsin_01_4.make-pin.pin INFO: Started Tue Jun 19 18:17:04 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_4.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 50695 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 40850 positives and 9845 negatives, size ratio=4.14931 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 17594 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 2 as initial direction. Could separate 17335 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 2 as initial direction. Could separate 17278 training set positives with q<0.01 in that direction. INFO: Found 26094 test set positives with q<0.01 in initial direction INFO: Reading in data and feature calculation took 2.40804 cpu seconds or 3 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 29248 PSMs with q<0.01 INFO: Iteration 2: Estimated 30011 PSMs with q<0.01 INFO: Iteration 3: Estimated 30096 PSMs with q<0.01 INFO: Iteration 4: Estimated 30143 PSMs with q<0.01 INFO: Iteration 5: Estimated 30136 PSMs with q<0.01 INFO: Iteration 6: Estimated 30131 PSMs with q<0.01 INFO: Iteration 7: Estimated 30123 PSMs with q<0.01 INFO: Iteration 8: Estimated 30116 PSMs with q<0.01 INFO: Iteration 9: Estimated 30122 PSMs with q<0.01 INFO: Iteration 10: Estimated 30114 PSMs with q<0.01 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -1.2665 -1.0858 -0.8618 lnrSp INFO: 2.7212 2.6632 2.4120 XCorr INFO: -0.0802 -0.0482 -0.1075 Sp INFO: 0.2263 0.2284 0.2423 IonFrac INFO: -0.4349 -0.2865 -0.3469 PepLen INFO: 0.0000 0.0000 0.0000 Charge1 INFO: -0.0595 -0.0208 -0.0400 Charge2 INFO: 0.0322 -0.0049 0.0287 Charge3 INFO: 0.0413 0.0623 0.0339 Charge4 INFO: 0.0533 -0.0389 -0.0359 Charge5 INFO: 0.0098 0.0063 0.0062 Charge6 INFO: 0.0000 0.0000 0.0000 enzN INFO: 0.0000 0.0000 0.0000 enzC INFO: -0.4694 -0.4318 -0.3259 enzInt INFO: -0.1137 -0.1361 -0.1340 lnNumDSP INFO: 0.3252 0.3754 0.3147 dM INFO: -0.1844 -0.1610 -0.1543 absdM INFO: 0.1456 -0.0366 -0.3752 m0 INFO: Found 30072 test set PSMs with q<0.01. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 40850 target PSMs and 9845 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 22039 target peptides with q<0.01. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 69.57 cpu seconds or 38 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 : 5.64389 cpu seconds or 6 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 = 0.7381448697 INFO: Number of protein groups identified at q-value = 0.01: 3801 INFO: Estimating protein probabilities took : 22.67 cpu seconds or 23 seconds wall clock time. INFO: Elapsed time: 67.3 s INFO: Finished crux percolator. INFO: Return Code:0