INFO: CPU: calc-server
INFO: Crux version: 3.1-4438655b
INFO: Sat Jun  9 17:03:52 MSK 2018
COMMAND LINE: crux percolator /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_3.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot 20100609_Velos1_TaGe_SA_293_4_3
INFO: Beginning percolator.
INFO: Reading file /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_3.comet.target.pep.xml
ERROR: Decoy file '/home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_3.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_3.comet.target.pep.xml
INFO: Assigning index 0 to /home/mark/overfit_test/comet/20100609_Velos1_TaGe_SA_293_4_3.comet.target.pep.xml.
INFO: There are 16712 target matches and 2715 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_3.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_3.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_3.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/20100609_Velos1_TaGe_SA_293_4_3.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_3.make-pin.pin
INFO: Started Sat Jun  9 17:03:53 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_3.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 19427 PSMs
INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
INFO: Train/test set contains 16712 positives and 2715 negatives, size ratio=6.15543 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 8823 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 8761 training set positives with q<0.01 in that direction.
INFO: Found 12991 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 0.165766 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 13725 PSMs with q<0.01
INFO: Iteration 2:	Estimated 13761 PSMs with q<0.01
INFO: Iteration 3:	Estimated 13759 PSMs with q<0.01
INFO: Iteration 4:	Estimated 13765 PSMs with q<0.01
INFO: Iteration 5:	Estimated 13759 PSMs with q<0.01
INFO: Iteration 6:	Estimated 13768 PSMs with q<0.01
INFO: Iteration 7:	Estimated 13761 PSMs with q<0.01
INFO: Iteration 8:	Estimated 13767 PSMs with q<0.01
INFO: Iteration 9:	Estimated 13761 PSMs with q<0.01
INFO: Iteration 10:	Estimated 13769 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO: -0.7318	-1.0060	-0.8775	lnrSp
INFO:  3.1884	 3.9527	 3.9252	XCorr
INFO: -0.1895	-0.2794	-0.2175	Sp
INFO:  0.1351	-0.1042	 0.0480	IonFrac
INFO:  0.0259	-0.2654	-0.0990	PepLen
INFO:  0.0000	 0.0000	 0.0000	Charge1
INFO:  0.1945	 0.2007	 0.2431	Charge2
INFO: -0.1626	-0.2067	-0.2062	Charge3
INFO: -0.1050	-0.0242	-0.0897	Charge4
INFO:  0.0892	 0.0350	 0.0110	Charge5
INFO:  0.0652	 0.1013	 0.0937	Charge6
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -0.3417	-0.3752	-0.3177	enzInt
INFO: -0.0776	-0.1811	-0.2066	lnNumDSP
INFO: -0.2921	-0.3556	-0.2248	dM
INFO: -0.5416	-0.5306	-0.4563	absdM
INFO:  1.5756	 1.8379	 1.9923	m0
INFO: Found 13737 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 16712 target PSMs and 2715 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 10562 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 8.542 cpu seconds or 5 seconds wall clock time.
INFO: Elapsed time: 6.14 s
INFO: Finished crux percolator.
INFO: Return Code:0