INFO: CPU: DESKTOP-52519M8
INFO: Crux version: 3.2-e786b8b
INFO: Mon 11/25/2019 
COMMAND LINE: crux pipeline --output-dir test_200_2000 --search-engine tide-search --precursor-window-type mz --precursor-window 0.6 --mz-bin-width 1.0005079 --add_C_cysteine +57.021464 --variable_mod01 +15.995 M 1 3 --max-precursor-charge 3 --precursor_charge 2 3 --num-threads 1 --override_charge 1 --overwrite T C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey1of3_1.raw C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey2of3_1.raw C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey3of3_1.raw human-index
INFO: Beginning pipeline.
INFO: Running pipeline with the following steps:
INFO: --> tide-search
INFO: --> percolator
INFO: Running tide-search...
INFO: Search will be run with the following files against database 'human-index':
INFO: --> C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey1of3_1.raw
INFO: --> C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey2of3_1.raw
INFO: --> C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey3of3_1.raw
INFO: Running tide-search...
INFO: Number of Threads: 1
INFO: Reading index human-index
INFO: Read 154527 target proteins
WARNING: The file 'test_200_2000/tide-search.target.txt' already exists and will be overwritten.
WARNING: The file 'test_200_2000/tide-search.decoy.txt' already exists and will be overwritten.
INFO: Converting C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey1of3_1.raw to spectrumrecords format
INFO: Elapsed time starting conversion: 3.02 s
WARNING: Spectrum 2 has no charge state. Calculating charge
INFO: Converting C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey2of3_1.raw to spectrumrecords format
INFO: Elapsed time starting conversion: 316 s
INFO: Converting C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey3of3_1.raw to spectrumrecords format
INFO: Elapsed time starting conversion: 544 s
INFO: Reading spectrum file test_200_2000/scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey1of3_1.raw.spectrumrecords.tmp.
INFO: Read 423210 spectra.
INFO: Starting search.
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INFO: [Thread 0]: Deleted 0 precursor, 0 isotope and 7817920 out-of-range peaks.
INFO: [Thread 0]: Retained 97.1706% of peaks.
INFO: Time per spectrum-charge combination: 0.004389 s.
INFO: Average number of candidates per spectrum-charge combination: -1932.151245 
INFO: Reading spectrum file test_200_2000/scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey2of3_1.raw.spectrumrecords.tmp.
INFO: Read 432192 spectra.
INFO: Starting search.
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INFO: [Thread 0]: Deleted 0 precursor, 0 isotope and 7591362 out-of-range peaks.
INFO: [Thread 0]: Retained 98.0543% of peaks.
INFO: Time per spectrum-charge combination: 0.009322 s.
INFO: Average number of candidates per spectrum-charge combination: -2098.422363 
INFO: Reading spectrum file test_200_2000/scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey3of3_1.raw.spectrumrecords.tmp.
INFO: Read 425329 spectra.
INFO: Starting search.
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INFO: [Thread 0]: Deleted 0 precursor, 0 isotope and 3229187 out-of-range peaks.
INFO: [Thread 0]: Retained 99.1566% of peaks.
INFO: Time per spectrum-charge combination: 0.012360 s.
INFO: Average number of candidates per spectrum-charge combination: -3307.714844 
INFO: Running percolator...
INFO: Post-processing will be run using the following files:
INFO: --> test_200_2000/tide-search.target.txt
INFO: --> test_200_2000/tide-search.decoy.txt
INFO: Running make-pin
INFO: Parsing test_200_2000/tide-search.target.txt
INFO: Assigning index 0 to C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey1of3_1.raw.
INFO: Assigning index 1 to C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey2of3_1.raw.
INFO: Assigning index 2 to C:\Users\enduser\Documents\ProteomeDiscoverer\191011_diaopt\1.5DaPrecursorTolerance\scanrange_200to2000_191010_Th_60min_DIA_200to2000_1Da_noOverlap_survey3of3_1.raw.
INFO: Parsing test_200_2000/tide-search.decoy.txt
INFO: There are 3132950 target matches and 2897956 decoys
INFO: Maximum observed charge is 3.
INFO: Finished make-pin.
INFO: Percolator version 3.02.0, Build Date May 30 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 test_200_2000/percolator.target.peptides.txt --decoy-results-peptides test_200_2000/percolator.decoy.peptides.txt --results-psms test_200_2000/percolator.target.psms.txt --decoy-results-psms test_200_2000/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 test_200_2000/make-pin.pin
INFO: Started Mon Nov 25 09:44:20 2019
INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
INFO: Reading tab-delimited input from datafile test_200_2000/make-pin.pin
INFO: Features:
INFO: XCorr PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumDSP dM absdM 
INFO: Found 6030906 PSMs
INFO: Separate target and decoy search inputs detected, using target-decoy competition on Percolator scores.
INFO: Train/test set contains 3132950 positives and 2897956 negatives, size ratio=1.08109 and pi0=1
INFO: Selecting Cpos by cross-validation.
INFO: Selecting Cneg by cross-validation.
INFO: Split 1:	Selected feature 1 as initial direction. Could separate 19040 training set positives with q<0.01 in that direction.
INFO: Split 2:	Selected feature 1 as initial direction. Could separate 19237 training set positives with q<0.01 in that direction.
INFO: Split 3:	Selected feature 1 as initial direction. Could separate 19357 training set positives with q<0.01 in that direction.
INFO: Found 28685 test set positives with q<0.01 in initial direction
INFO: Reading in data and feature calculation took 103.608 cpu seconds or 104 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 44128 PSMs with q<0.01
INFO: Iteration 2:	Estimated 49311 PSMs with q<0.01
INFO: Iteration 3:	Estimated 50743 PSMs with q<0.01
INFO: Iteration 4:	Estimated 51241 PSMs with q<0.01
INFO: Iteration 5:	Estimated 51311 PSMs with q<0.01
INFO: Iteration 6:	Estimated 51330 PSMs with q<0.01
INFO: Iteration 7:	Estimated 51333 PSMs with q<0.01
INFO: Iteration 8:	Estimated 51263 PSMs with q<0.01
INFO: Iteration 9:	Estimated 51280 PSMs with q<0.01
INFO: Iteration 10:	Estimated 51259 PSMs with q<0.01
INFO: Learned normalized SVM weights for the 3 cross-validation splits:
INFO:  Split1	 Split2	 Split3	FeatureName
INFO:  1.7111	 2.1028	 1.8764	XCorr
INFO: -0.5021	-0.5764	-0.6908	PepLen
INFO: -0.2129	-0.2539	-0.4124	Charge1
INFO:  0.4920	 0.6159	 0.4019	Charge2
INFO: -0.3776	-0.4794	-0.1802	Charge3
INFO:  0.0000	 0.0000	 0.0000	enzN
INFO:  0.0000	 0.0000	 0.0000	enzC
INFO: -1.7248	-2.2543	-1.6443	enzInt
INFO:  0.9216	 1.2994	 0.4885	lnNumDSP
INFO: -0.0590	-0.0291	-0.0389	dM
INFO:  0.1455	 0.2207	 0.2072	absdM
INFO: -6.4965	-7.9136	-6.4561	m0
INFO: Found 51019 test set PSMs with q<0.01.
INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 685224 target PSMs and 521006 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 18162 target peptides with q<0.01.
INFO: Calculating posterior error probabilities (PEPs).
INFO: Processing took 2109 cpu seconds or 2109 seconds wall clock time.
INFO: Elapsed time: 7.95e+003 s
INFO: Finished crux pipeline.
INFO: Return Code:0