INFO: CPU: calc-server INFO: Crux version: 3.1-4438655b INFO: Sat Jun 9 17:05:17 MSK 2018 COMMAND LINE: crux percolator /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_7.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot olsen_100ng_30min_15k_01_7 INFO: Beginning percolator. INFO: Reading file /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_7.comet.target.pep.xml ERROR: Decoy file '/home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_7.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_7.comet.target.pep.xml INFO: Assigning index 0 to /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_7.comet.target.pep.xml. INFO: There are 21336 target matches and 4770 decoys INFO: Maximum observed charge is 5. 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/olsen_100ng_30min_15k_01_7.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_7.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_7.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_7.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/olsen_100ng_30min_15k_01_7.make-pin.pin INFO: Started Sat Jun 9 17:05:18 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/olsen_100ng_30min_15k_01_7.make-pin.pin INFO: Features: INFO: lnrSp XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt lnNumDSP dM absdM INFO: Found 26106 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 21336 positives and 4770 negatives, size ratio=4.47296 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 9151 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 2 as initial direction. Could separate 8968 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 2 as initial direction. Could separate 8998 training set positives with q<0.01 in that direction. INFO: Found 13572 test set positives with q<0.01 in initial direction INFO: Reading in data and feature calculation took 0.218416 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 15007 PSMs with q<0.01 INFO: Iteration 2: Estimated 15249 PSMs with q<0.01 INFO: Iteration 3: Estimated 15359 PSMs with q<0.01 INFO: Iteration 4: Estimated 15361 PSMs with q<0.01 INFO: Iteration 5: Estimated 15350 PSMs with q<0.01 INFO: Iteration 6: Estimated 15327 PSMs with q<0.01 INFO: Iteration 7: Estimated 15339 PSMs with q<0.01 INFO: Iteration 8: Estimated 15342 PSMs with q<0.01 INFO: Iteration 9: Estimated 15348 PSMs with q<0.01 INFO: Iteration 10: Estimated 15347 PSMs with q<0.01 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -1.6991 -1.6500 -1.8402 lnrSp INFO: 2.5810 2.4409 2.8043 XCorr INFO: -0.0170 0.1817 0.0115 Sp INFO: -0.1423 -0.2796 -0.1998 IonFrac INFO: 0.2750 0.3548 0.4707 PepLen INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.2186 0.2536 0.2463 Charge2 INFO: -0.0015 0.0340 0.0745 Charge3 INFO: -0.2342 -0.3044 -0.3751 Charge4 INFO: -0.2130 -0.2926 -0.2508 Charge5 INFO: 0.0000 0.0000 0.0000 enzN INFO: 0.0000 0.0000 0.0000 enzC INFO: -0.6127 -0.5914 -0.8261 enzInt INFO: -0.0131 0.0589 0.0656 lnNumDSP INFO: -0.1527 -0.1803 -0.2718 dM INFO: -0.4436 -0.5130 -0.6794 absdM INFO: -0.1893 -0.1545 0.1135 m0 INFO: Found 15328 test set PSMs with q<0.01. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 21336 target PSMs and 4770 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 13255 target peptides with q<0.01. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 10.07 cpu seconds or 5 seconds wall clock time. INFO: Elapsed time: 7.23 s INFO: Finished crux percolator. INFO: Return Code:0