INFO: CPU: calc-server INFO: Crux version: 3.1-4438655b INFO: Sat Jun 9 17:05:11 MSK 2018 COMMAND LINE: crux percolator /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_2.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot 20100609_Velos1_TaGe_SA_293_4_2 INFO: Beginning percolator. INFO: Reading file /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_2.comet.target.pep.xml ERROR: Decoy file '/home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_2.comet.decoy.pep.xml' doesn't exist INFO: Converting input to pin format. INFO: Parsing /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_2.comet.target.pep.xml INFO: Assigning index 0 to /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_2.comet.target.pep.xml. INFO: There are 16593 target matches and 2833 decoys INFO: Maximum observed charge is 6. INFO: File conversion complete. INFO: Percolator version 3.02.0, Build Date Apr 5 2018 13:54:08 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/20100609_Velos1_TaGe_SA_293_4_2.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_2.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_2.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_2.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 --post-processing-tdc /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_2.make-pin.pin INFO: Started Sat Jun 9 17:05:12 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/20100609_Velos1_TaGe_SA_293_4_2.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 19426 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 16593 positives and 2833 negatives, size ratio=5.85704 and pi0=1 INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 3 as initial direction. Could separate 8803 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 2 as initial direction. Could separate 8779 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 2 as initial direction. Could separate 8797 training set positives with q<0.01 in that direction. INFO: Found 13004 test set positives with q<0.01 in initial direction INFO: Reading in data and feature calculation took 0.165391 cpu seconds or 0 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 13759 PSMs with q<0.01 INFO: Iteration 2: Estimated 13832 PSMs with q<0.01 INFO: Iteration 3: Estimated 13824 PSMs with q<0.01 INFO: Iteration 4: Estimated 13828 PSMs with q<0.01 INFO: Iteration 5: Estimated 13821 PSMs with q<0.01 INFO: Iteration 6: Estimated 13826 PSMs with q<0.01 INFO: Iteration 7: Estimated 13828 PSMs with q<0.01 INFO: Iteration 8: Estimated 13827 PSMs with q<0.01 INFO: Iteration 9: Estimated 13825 PSMs with q<0.01 INFO: Iteration 10: Estimated 13828 PSMs with q<0.01 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -1.0656 -0.9905 -1.2243 lnrSp INFO: 3.0899 3.2593 4.0482 XCorr INFO: 0.0363 0.1001 -0.1853 Sp INFO: -0.0338 -0.0821 -0.0601 IonFrac INFO: -0.1339 -0.0473 -0.1781 PepLen INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.1335 0.2155 0.1825 Charge2 INFO: -0.1611 -0.1492 -0.1653 Charge3 INFO: 0.0128 -0.1405 -0.0557 Charge4 INFO: 0.0624 0.0180 0.0293 Charge5 INFO: 0.0407 0.0865 0.0578 Charge6 INFO: 0.0000 0.0000 0.0000 enzN INFO: 0.0000 0.0000 0.0000 enzC INFO: -0.2497 -0.1863 -0.3000 enzInt INFO: 0.0152 -0.0512 -0.1010 lnNumDSP INFO: -0.5151 -0.3471 -0.5039 dM INFO: -0.5846 -0.5460 -0.6117 absdM INFO: 1.5757 1.8425 2.0263 m0 INFO: Found 13815 test set PSMs with q<0.01. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 16593 target PSMs and 2833 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 10565 target peptides with q<0.01. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 8.508 cpu seconds or 5 seconds wall clock time. INFO: Elapsed time: 6.08 s INFO: Finished crux percolator. INFO: Return Code:0