INFO: CPU: calc-server
INFO: Crux version: 3.1-4438655b
INFO: Sat Jun  9 17:04:27 MSK 2018
COMMAND LINE: crux percolator /home/mark/overfit_test/comet/confetti_trypsin_01_9.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot confetti_trypsin_01_9
INFO: Beginning percolator.
INFO: Reading file /home/mark/overfit_test/comet/confetti_trypsin_01_9.comet.target.pep.xml
ERROR: Decoy file '/home/mark/overfit_test/comet/confetti_trypsin_01_9.comet.decoy.pep.xml' doesn't exist
INFO: Converting input to pin format.
INFO: Parsing /home/mark/overfit_test/comet/confetti_trypsin_01_9.comet.target.pep.xml
INFO: Assigning index 0 to /home/mark/overfit_test/comet/confetti_trypsin_01_9.comet.target.pep.xml.
INFO: There are 40916 target matches and 9776 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_9.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_9.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_9.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/confetti_trypsin_01_9.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_9.make-pin.pin
INFO: Started Sat Jun  9 17:04:30 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_9.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 50692 PSMs
INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
INFO: Train/test set contains 40916 positives and 9776 negatives, size ratio=4.18535 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 17660 training set positives with q<0.01 in that direction.
INFO: Split 2:	Selected feature 2 as initial direction. Could separate 17440 training set positives with q<0.01 in that direction.
INFO: Split 3:	Selected feature 2 as initial direction. Could separate 17437 training set positives with q<0.01 in that direction.
INFO: Found 26240 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 0.505666 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 29304 PSMs with q<0.01
INFO: Iteration 2:	Estimated 30003 PSMs with q<0.01
INFO: Iteration 3:	Estimated 30170 PSMs with q<0.01
INFO: Iteration 4:	Estimated 30171 PSMs with q<0.01
INFO: Iteration 5:	Estimated 30190 PSMs with q<0.01
INFO: Iteration 6:	Estimated 30183 PSMs with q<0.01
INFO: Iteration 7:	Estimated 30181 PSMs with q<0.01
INFO: Iteration 8:	Estimated 30189 PSMs with q<0.01
INFO: Iteration 9:	Estimated 30174 PSMs with q<0.01
INFO: Iteration 10:	Estimated 30186 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO: -1.3494	-1.5506	-1.6052	lnrSp
INFO:  3.0706	 3.0157	 3.1487	XCorr
INFO: -0.2967	-0.0577	-0.2431	Sp
INFO:  0.2881	 0.3451	 0.3317	IonFrac
INFO: -0.4193	-0.2379	-0.4131	PepLen
INFO:  0.0000	 0.0000	 0.0000	Charge1
INFO: -0.0408	-0.0300	-0.0473	Charge2
INFO: -0.0071	-0.0034	 0.0030	Charge3
INFO:  0.0893	 0.0607	 0.0855	Charge4
INFO:  0.0249	 0.0247	 0.0161	Charge5
INFO:  0.0046	-0.0037	-0.0027	Charge6
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -0.4823	-0.4343	-0.4714	enzInt
INFO: -0.2205	-0.1832	-0.2370	lnNumDSP
INFO:  0.3113	 0.3492	 0.3161	dM
INFO: -0.1313	-0.2095	-0.1743	absdM
INFO:  0.2110	 0.2227	 0.1648	m0
INFO: Found 30053 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 40916 target PSMs and 9776 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 22043 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 20.86 cpu seconds or 9 seconds wall clock time.
INFO: Elapsed time: 13.2 s
INFO: Finished crux percolator.
INFO: Return Code:0