INFO: CPU: calc-server
INFO: Crux version: 3.1-4438655b
INFO: Sat Jun  9 17:02:48 MSK 2018
COMMAND LINE: crux percolator /home/mark/overfit_test/comet/confetti_trypsin_01_1.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot confetti_trypsin_01_1
INFO: Beginning percolator.
INFO: Reading file /home/mark/overfit_test/comet/confetti_trypsin_01_1.comet.target.pep.xml
ERROR: Decoy file '/home/mark/overfit_test/comet/confetti_trypsin_01_1.comet.decoy.pep.xml' doesn't exist
INFO: Converting input to pin format.
INFO: Parsing /home/mark/overfit_test/comet/confetti_trypsin_01_1.comet.target.pep.xml
INFO: Assigning index 0 to /home/mark/overfit_test/comet/confetti_trypsin_01_1.comet.target.pep.xml.
INFO: There are 40923 target matches and 9771 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/confetti_trypsin_01_1.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_1.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_1.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/confetti_trypsin_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 --post-processing-tdc /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_1.make-pin.pin
INFO: Started Sat Jun  9 17:02:51 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/confetti_trypsin_01_1.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 50694 PSMs
INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
INFO: Train/test set contains 40923 positives and 9771 negatives, size ratio=4.18821 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 17893 training set positives with q<0.01 in that direction.
INFO: Split 2:	Selected feature 2 as initial direction. Could separate 17818 training set positives with q<0.01 in that direction.
INFO: Split 3:	Selected feature 2 as initial direction. Could separate 17746 training set positives with q<0.01 in that direction.
INFO: Found 26707 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 0.501467 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 29496 PSMs with q<0.01
INFO: Iteration 2:	Estimated 30100 PSMs with q<0.01
INFO: Iteration 3:	Estimated 30284 PSMs with q<0.01
INFO: Iteration 4:	Estimated 30351 PSMs with q<0.01
INFO: Iteration 5:	Estimated 30355 PSMs with q<0.01
INFO: Iteration 6:	Estimated 30342 PSMs with q<0.01
INFO: Iteration 7:	Estimated 30345 PSMs with q<0.01
INFO: Iteration 8:	Estimated 30343 PSMs with q<0.01
INFO: Iteration 9:	Estimated 30341 PSMs with q<0.01
INFO: Iteration 10:	Estimated 30340 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO: -1.8638	-1.8572	-1.5778	lnrSp
INFO:  3.1444	 3.4018	 2.6926	XCorr
INFO: -0.3283	-0.4131	-0.2376	Sp
INFO:  0.3349	 0.2994	 0.2287	IonFrac
INFO: -0.2942	-0.3164	-0.2600	PepLen
INFO:  0.0000	 0.0000	 0.0000	Charge1
INFO: -0.0411	 0.0074	-0.0112	Charge2
INFO:  0.0184	 0.0013	 0.0113	Charge3
INFO:  0.0336	-0.0276	-0.0125	Charge4
INFO:  0.0475	 0.0365	 0.0446	Charge5
INFO: -0.0013	-0.0016	 0.0033	Charge6
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -0.4626	-0.4324	-0.4075	enzInt
INFO: -0.1843	-0.1567	-0.1474	lnNumDSP
INFO:  0.3210	 0.3408	 0.2489	dM
INFO: -0.1815	-0.2414	-0.1569	absdM
INFO:  0.0782	 0.0959	-0.1986	m0
INFO: Found 30304 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 40923 target PSMs and 9771 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 22217 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 20.02 cpu seconds or 9 seconds wall clock time.
INFO: Elapsed time: 13 s
INFO: Finished crux percolator.
INFO: Return Code:0