INFO: CPU: calc-server
INFO: Crux version: 3.1-4438655b
INFO: Sat Jun  9 17:06:49 MSK 2018
COMMAND LINE: crux percolator /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_4.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot 20100609_Velos1_TaGe_SA_293_4_4
INFO: Beginning percolator.
INFO: Reading file /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_4.comet.target.pep.xml
ERROR: Decoy file '/home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_4.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_4.comet.target.pep.xml
INFO: Assigning index 0 to /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_4.comet.target.pep.xml.
INFO: There are 16649 target matches and 2783 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_4.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_4.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_4.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_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 --post-processing-tdc /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_4.make-pin.pin
INFO: Started Sat Jun  9 17:06:50 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_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 19432 PSMs
INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
INFO: Train/test set contains 16649 positives and 2783 negatives, size ratio=5.98239 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 8820 training set positives with q<0.01 in that direction.
INFO: Split 2:	Selected feature 2 as initial direction. Could separate 8692 training set positives with q<0.01 in that direction.
INFO: Split 3:	Selected feature 2 as initial direction. Could separate 8828 training set positives with q<0.01 in that direction.
INFO: Found 13171 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 0.16623 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 13696 PSMs with q<0.01
INFO: Iteration 2:	Estimated 13718 PSMs with q<0.01
INFO: Iteration 3:	Estimated 13713 PSMs with q<0.01
INFO: Iteration 4:	Estimated 13719 PSMs with q<0.01
INFO: Iteration 5:	Estimated 13717 PSMs with q<0.01
INFO: Iteration 6:	Estimated 13718 PSMs with q<0.01
INFO: Iteration 7:	Estimated 13719 PSMs with q<0.01
INFO: Iteration 8:	Estimated 13720 PSMs with q<0.01
INFO: Iteration 9:	Estimated 13720 PSMs with q<0.01
INFO: Iteration 10:	Estimated 13720 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO: -2.5580	-2.6752	-0.1729	lnrSp
INFO:  3.8594	 3.5900	 2.8647	XCorr
INFO:  0.0932	-0.1138	 0.7021	Sp
INFO: -0.2307	 0.1820	-0.1061	IonFrac
INFO: -0.1828	 0.0613	-0.0067	PepLen
INFO:  0.0000	 0.0000	 0.0000	Charge1
INFO:  0.2762	 0.2188	 0.2427	Charge2
INFO: -0.2744	-0.1540	-0.1732	Charge3
INFO: -0.0326	-0.1360	-0.1454	Charge4
INFO:  0.0120	 0.0126	 0.0266	Charge5
INFO:  0.1033	 0.0860	 0.0425	Charge6
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -0.2091	-0.2776	-0.2781	enzInt
INFO: -0.1605	-0.1710	-0.1098	lnNumDSP
INFO: -1.0780	-0.7260	-0.9715	dM
INFO: -1.0948	-0.7913	-0.8825	absdM
INFO:  1.0442	 1.1856	 1.2735	m0
INFO: Found 13667 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 16649 target PSMs and 2783 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 10476 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 13.4 cpu seconds or 10 seconds wall clock time.
INFO: Elapsed time: 10.9 s
INFO: Finished crux percolator.
INFO: Return Code:0