INFO: CPU: calc-server INFO: Crux version: 3.1-f2e7488 INFO: Tue Jun 19 18:03:32 MSK 2018 COMMAND LINE: /home/mark/crux/bin/crux percolator /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_1.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet_proteins --fileroot olsen_100ng_30min_15k_01_1 --protein T --overwrite T --fido-empirical-protein-q T --protein-report-duplicates T INFO: Beginning percolator. INFO: Reading file /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_1.comet.target.pep.xml ERROR: Decoy file '/home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_1.comet.decoy.pep.xml' doesn't exist INFO: Converting input to pin format. INFO: Parsing /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_1.comet.target.pep.xml INFO: Assigning index 0 to /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_1.comet.target.pep.xml. INFO: There are 21329 target matches and 4780 decoys INFO: Maximum observed charge is 5. 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/olsen_100ng_30min_15k_01_1.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet_proteins/olsen_100ng_30min_15k_01_1.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet_proteins/olsen_100ng_30min_15k_01_1.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet_proteins/olsen_100ng_30min_15k_01_1.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/olsen_100ng_30min_15k_01_1.percolator.target.proteins.txt --decoy-results-proteins /home/mark/overfit_test/percolator_comet_proteins/olsen_100ng_30min_15k_01_1.percolator.decoy.proteins.txt --post-processing-tdc /home/mark/overfit_test/percolator_comet_proteins/olsen_100ng_30min_15k_01_1.make-pin.pin INFO: Started Tue Jun 19 18:03:34 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/olsen_100ng_30min_15k_01_1.make-pin.pin INFO: Features: INFO: lnrSp XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt lnNumDSP dM absdM INFO: Found 26109 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 21329 positives and 4780 negatives, size ratio=4.46213 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 8953 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 2 as initial direction. Could separate 8972 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 2 as initial direction. Could separate 8933 training set positives with q<0.01 in that direction. INFO: Found 13422 test set positives with q<0.01 in initial direction INFO: Reading in data and feature calculation took 1.04914 cpu seconds or 1 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 14818 PSMs with q<0.01 INFO: Iteration 2: Estimated 15086 PSMs with q<0.01 INFO: Iteration 3: Estimated 15161 PSMs with q<0.01 INFO: Iteration 4: Estimated 15173 PSMs with q<0.01 INFO: Iteration 5: Estimated 15169 PSMs with q<0.01 INFO: Iteration 6: Estimated 15165 PSMs with q<0.01 INFO: Iteration 7: Estimated 15165 PSMs with q<0.01 INFO: Iteration 8: Estimated 15168 PSMs with q<0.01 INFO: Iteration 9: Estimated 15167 PSMs with q<0.01 INFO: Iteration 10: Estimated 15165 PSMs with q<0.01 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -1.1109 -1.6180 -1.2604 lnrSp INFO: 2.4729 2.6232 2.3508 XCorr INFO: 0.0672 -0.0273 0.1631 Sp INFO: -0.3169 -0.2341 -0.2823 IonFrac INFO: 0.3269 0.4240 0.2923 PepLen INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.2494 0.2651 0.1924 Charge2 INFO: 0.0468 0.0751 0.0405 Charge3 INFO: -0.3442 -0.3739 -0.2459 Charge4 INFO: -0.2369 -0.3159 -0.2377 Charge5 INFO: 0.0000 0.0000 0.0000 enzN INFO: 0.0000 0.0000 0.0000 enzC INFO: -0.6264 -0.8202 -0.7289 enzInt INFO: -0.0468 -0.0150 0.0252 lnNumDSP INFO: -0.0057 -0.0160 -0.1357 dM INFO: -0.5278 -0.6465 -0.5884 absdM INFO: -0.0238 0.0868 0.1833 m0 INFO: Found 15076 test set PSMs with q<0.01. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 21329 target PSMs and 4780 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 13094 target peptides with q<0.01. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 60.36 cpu seconds or 46 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 : 3.2623 cpu seconds or 3 seconds wall time INFO: The following parameters have been chosen: INFO: alpha = 0.032 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 = 0.7237108492 INFO: Number of protein groups identified at q-value = 0.01: 2342 INFO: Estimating protein probabilities took : 14.37 cpu seconds or 15 seconds wall clock time. INFO: Elapsed time: 63.6 s INFO: Finished crux percolator. INFO: Return Code:0