INFO: CPU: calc-server
INFO: Crux version: 3.1-4438655b
INFO: Sat Jun  9 17:06:15 MSK 2018
COMMAND LINE: crux percolator /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_4.comet.target.pep.xml --decoy-prefix DECOY_ --output-dir /home/mark/overfit_test/percolator_comet --fileroot olsen_100ng_30min_15k_01_4
INFO: Beginning percolator.
INFO: Reading file /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_4.comet.target.pep.xml
ERROR: Decoy file '/home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_4.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_4.comet.target.pep.xml
INFO: Assigning index 0 to /home/mark/overfit_test/comet/olsen_100ng_30min_15k_01_4.comet.target.pep.xml.
INFO: There are 21325 target matches and 4785 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_4.percolator.target.peptides.txt --decoy-results-peptides /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_4.percolator.decoy.peptides.txt --results-psms /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_4.percolator.target.psms.txt --decoy-results-psms /home/mark/overfit_test/percolator_comet/olsen_100ng_30min_15k_01_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/olsen_100ng_30min_15k_01_4.make-pin.pin
INFO: Started Sat Jun  9 17:06:17 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_4.make-pin.pin
INFO: Features:
INFO: lnrSp XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 Charge4 Charge5 enzN enzC enzInt lnNumDSP dM absdM 
INFO: Found 26110 PSMs
INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
INFO: Train/test set contains 21325 positives and 4785 negatives, size ratio=4.45664 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 9139 training set positives with q<0.01 in that direction.
INFO: Split 2:	Selected feature 2 as initial direction. Could separate 8714 training set positives with q<0.01 in that direction.
INFO: Split 3:	Selected feature 2 as initial direction. Could separate 8748 training set positives with q<0.01 in that direction.
INFO: Found 13330 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 0.217055 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 14739 PSMs with q<0.01
INFO: Iteration 2:	Estimated 15045 PSMs with q<0.01
INFO: Iteration 3:	Estimated 15136 PSMs with q<0.01
INFO: Iteration 4:	Estimated 15159 PSMs with q<0.01
INFO: Iteration 5:	Estimated 15182 PSMs with q<0.01
INFO: Iteration 6:	Estimated 15195 PSMs with q<0.01
INFO: Iteration 7:	Estimated 15203 PSMs with q<0.01
INFO: Iteration 8:	Estimated 15219 PSMs with q<0.01
INFO: Iteration 9:	Estimated 15213 PSMs with q<0.01
INFO: Iteration 10:	Estimated 15213 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO: -1.1054	-1.4591	-1.2885	lnrSp
INFO:  2.4181	 2.5571	 2.4889	XCorr
INFO:  0.0259	 0.1133	 0.0568	Sp
INFO: -0.1608	-0.1211	-0.0802	IonFrac
INFO:  0.2600	 0.3437	 0.3422	PepLen
INFO:  0.0000	 0.0000	 0.0000	Charge1
INFO:  0.1900	 0.1344	 0.1528	Charge2
INFO:  0.0177	 0.0520	 0.0266	Charge3
INFO: -0.2292	-0.1826	-0.1774	Charge4
INFO: -0.1924	-0.2195	-0.2087	Charge5
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -0.6361	-0.8152	-0.7067	enzInt
INFO: -0.0199	-0.0526	-0.0094	lnNumDSP
INFO: -0.1564	-0.2064	-0.0908	dM
INFO: -0.5916	-0.6527	-0.6652	absdM
INFO:  0.3507	 0.1412	 0.1543	m0
INFO: Found 15088 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 21325 target PSMs and 4785 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 13080 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 9.855 cpu seconds or 5 seconds wall clock time.
INFO: Elapsed time: 7.15 s
INFO: Finished crux percolator.
INFO: Return Code:0