[2021/11/30 14:22:31] [2021/11/30 14:22:31] Detecting decoy prefix in decoy_2021-02-24-reviewed-contam-UP000005640.fasta. [2021/11/30 14:22:33] Some common prefixes were found: DECOY: 50.0 % DEC: 50.0 % Using DECOY as the most likely decoy prefix. [2021/11/30 14:22:34] MSFragger version MSFragger-3.4 [2021/11/30 14:22:34] Batmass-IO version 1.23.6 [2021/11/30 14:22:34] timsdata library version timsdata-2-8-7-1 [2021/11/30 14:22:34] (c) University of Michigan [2021/11/30 14:22:34] RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. [2021/11/30 14:22:34] System OS: Windows 10, Architecture: AMD64 [2021/11/30 14:22:34] Java Info: 17.0.1, OpenJDK 64-Bit Server VM, Oracle Corporation [2021/11/30 14:22:34] JVM started with 15 GB memory [2021/11/30 14:22:34] Checking database... [2021/11/30 14:22:35] Checking spectral files... [2021/11/30 14:22:35] E:\08232021.plasma\08052021_sjr_0090.d: Scans = 7482 [2021/11/30 14:22:35] E:\08232021.plasma\08052021_sjr_0092.d: Scans = 6504 [2021/11/30 14:22:35] E:\08232021.plasma\08052021_sjr_0091.d: Scans = 8026 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0096.d: Scans = 7222 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0097.d: Scans = 7199 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0094.d: Scans = 7558 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0095.d: Scans = 7450 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0093.d: Scans = 8266 [2021/11/30 14:22:39] E:\08232021.plasma\08052021_sjr_0098.d: Scans = 7514 [2021/11/30 14:22:39] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0090.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:39] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0091.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:39] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0092.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0093.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0094.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0095.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0096.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0097.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] There is a mzBIN file from E:\08232021.plasma\08052021_sjr_0098.d converted with timsdata-2-8-7-1. Will use this mzBIN file. [2021/11/30 14:22:40] [2021/11/30 14:22:40] ************************************MAIN SEARCH************************************ [2021/11/30 14:22:40] Checking database... [2021/11/30 14:22:41] Parameters: [2021/11/30 14:22:41] num_threads = 8 [2021/11/30 14:22:41] database_name = M:\Software\FragPipe-14.0\decoy_2021-02-24-reviewed-contam-UP000005640.fasta [2021/11/30 14:22:41] decoy_prefix = DECOY [2021/11/30 14:22:41] precursor_mass_lower = -50.0 [2021/11/30 14:22:41] precursor_mass_upper = 50.0 [2021/11/30 14:22:41] precursor_mass_units = 1 [2021/11/30 14:22:41] data_type = 0 [2021/11/30 14:22:41] precursor_true_tolerance = 20.0 [2021/11/30 14:22:41] precursor_true_units = 1 [2021/11/30 14:22:41] fragment_mass_tolerance = 20.0 [2021/11/30 14:22:41] fragment_mass_units = 1 [2021/11/30 14:22:41] calibrate_mass = 0 [2021/11/30 14:22:41] use_all_mods_in_first_search = false [2021/11/30 14:22:41] write_calibrated_mgf = 0 [2021/11/30 14:22:41] isotope_error = 0/1/2/3 [2021/11/30 14:22:41] mass_offsets = 0 [2021/11/30 14:22:41] labile_search_mode = OFF [2021/11/30 14:22:41] restrict_deltamass_to = all [2021/11/30 14:22:41] precursor_mass_mode = SELECTED [2021/11/30 14:22:41] localize_delta_mass = false [2021/11/30 14:22:41] delta_mass_exclude_ranges = (-1.5,3.5) [2021/11/30 14:22:41] fragment_ion_series = b,y [2021/11/30 14:22:41] ion_series_definitions = [2021/11/30 14:22:41] search_enzyme_name = Trypsin [2021/11/30 14:22:41] search_enzyme_sense_1 = C [2021/11/30 14:22:41] search_enzyme_cut_1 = KR [2021/11/30 14:22:41] search_enzyme_nocut_1 = P [2021/11/30 14:22:41] allowed_missed_cleavage_1 = 1 [2021/11/30 14:22:41] num_enzyme_termini = 2 [2021/11/30 14:22:41] clip_nTerm_M = true [2021/11/30 14:22:41] allow_multiple_variable_mods_on_residue = false [2021/11/30 14:22:41] max_variable_mods_per_peptide = 3 [2021/11/30 14:22:41] max_variable_mods_combinations = 5500 [2021/11/30 14:22:41] output_format = pepxml_pin [2021/11/30 14:22:41] output_report_topN = 1 [2021/11/30 14:22:41] output_max_expect = 50.0 [2021/11/30 14:22:41] report_alternative_proteins = true [2021/11/30 14:22:41] override_charge = false [2021/11/30 14:22:41] precursor_charge_low = 1 [2021/11/30 14:22:41] precursor_charge_high = 4 [2021/11/30 14:22:41] digest_min_length = 5 [2021/11/30 14:22:41] digest_max_length = 60 [2021/11/30 14:22:41] digest_mass_range_low = 200.0 [2021/11/30 14:22:41] digest_mass_range_high = 5000.0 [2021/11/30 14:22:41] max_fragment_charge = 2 [2021/11/30 14:22:41] deisotope = 1 [2021/11/30 14:22:41] deneutralloss = true [2021/11/30 14:22:41] track_zero_topN = 0 [2021/11/30 14:22:41] zero_bin_accept_expect = 0.0 [2021/11/30 14:22:41] zero_bin_mult_expect = 1.0 [2021/11/30 14:22:41] add_topN_complementary = 0 [2021/11/30 14:22:41] minimum_peaks = 15 [2021/11/30 14:22:41] use_topN_peaks = 50 [2021/11/30 14:22:41] minIonsScoring = 2 [2021/11/30 14:22:41] min_matched_fragments = 4 [2021/11/30 14:22:41] minimum_ratio = 0.01 [2021/11/30 14:22:41] intensity_transform = 0 [2021/11/30 14:22:41] remove_precursor_peak = 1 [2021/11/30 14:22:41] remove_precursor_range = -1.500000,1.500000 [2021/11/30 14:22:41] clear_mz_range_low = 0.0 [2021/11/30 14:22:41] clear_mz_range_high = 0.0 [2021/11/30 14:22:41] excluded_scan_list_file = [2021/11/30 14:22:41] mass_diff_to_variable_mod = 0 [2021/11/30 14:22:41] min_sequence_matches = 2 [2021/11/30 14:22:41] check_spectral_files = true [2021/11/30 14:22:41] variable_mod_01 = 42.010565 n^ 3 [2021/11/30 14:22:41] variable_mod_02 = 15.994915 M 3 [2021/11/30 14:22:41] add_C_cysteine = 57.021464 [2021/11/30 14:22:41] add_Cterm_peptide = 0.0 [2021/11/30 14:22:41] add_Cterm_protein = 0.0 [2021/11/30 14:22:41] add_Nterm_peptide = 0.0 [2021/11/30 14:22:41] add_Nterm_protein = 0.0 [2021/11/30 14:22:42] Number of unique peptides [2021/11/30 14:22:45] of length 5: 131575 [2021/11/30 14:22:45] of length 6: 212599 [2021/11/30 14:22:45] of length 7: 217686 [2021/11/30 14:22:45] of length 8: 201884 [2021/11/30 14:22:45] of length 9: 193754 [2021/11/30 14:22:45] of length 10: 177280 [2021/11/30 14:22:45] of length 11: 163103 [2021/11/30 14:22:45] of length 12: 151026 [2021/11/30 14:22:45] of length 13: 142776 [2021/11/30 14:22:45] of length 14: 128107 [2021/11/30 14:22:45] of length 15: 119930 [2021/11/30 14:22:45] of length 16: 109393 [2021/11/30 14:22:45] of length 17: 100141 [2021/11/30 14:22:45] of length 18: 93276 [2021/11/30 14:22:45] of length 19: 87567 [2021/11/30 14:22:45] of length 20: 79528 [2021/11/30 14:22:45] of length 21: 74393 [2021/11/30 14:22:45] of length 22: 68130 [2021/11/30 14:22:45] of length 23: 63244 [2021/11/30 14:22:45] of length 24: 59283 [2021/11/30 14:22:45] of length 25: 54941 [2021/11/30 14:22:45] of length 26: 50378 [2021/11/30 14:22:45] of length 27: 47809 [2021/11/30 14:22:45] of length 28: 44575 [2021/11/30 14:22:45] of length 29: 40963 [2021/11/30 14:22:45] of length 30: 38141 [2021/11/30 14:22:45] of length 31: 35170 [2021/11/30 14:22:45] of length 32: 32912 [2021/11/30 14:22:45] of length 33: 30253 [2021/11/30 14:22:45] of length 34: 27913 [2021/11/30 14:22:45] of length 35: 25416 [2021/11/30 14:22:45] of length 36: 24282 [2021/11/30 14:22:45] of length 37: 21533 [2021/11/30 14:22:45] of length 38: 20138 [2021/11/30 14:22:45] of length 39: 17936 [2021/11/30 14:22:45] of length 40: 17090 [2021/11/30 14:22:45] of length 41: 16076 [2021/11/30 14:22:45] of length 42: 14301 [2021/11/30 14:22:45] of length 43: 12518 [2021/11/30 14:22:45] of length 44: 10068 [2021/11/30 14:22:45] of length 45: 7886 [2021/11/30 14:22:45] of length 46: 5322 [2021/11/30 14:22:45] of length 47: 3471 [2021/11/30 14:22:45] of length 48: 2130 [2021/11/30 14:22:45] of length 49: 1116 [2021/11/30 14:22:45] of length 50: 703 [2021/11/30 14:22:45] of length 51: 438 [2021/11/30 14:22:45] of length 52: 235 [2021/11/30 14:22:45] of length 53: 140 [2021/11/30 14:22:45] of length 54: 74 [2021/11/30 14:22:45] of length 55: 52 [2021/11/30 14:22:45] of length 56: 35 [2021/11/30 14:22:45] of length 57: 15 [2021/11/30 14:22:45] of length 58: 6 [2021/11/30 14:22:45] of length 59: 8 [2021/11/30 14:22:45] of length 60: 4 [2021/11/30 14:22:45] In total 3178723 peptides. [2021/11/30 14:22:47] Generated 8986264 modified peptides. [2021/11/30 14:22:47] Number of peptides with more than 5500 modification patterns: 0 [2021/11/30 14:23:36] Selected fragment index width 0.10 Da. [2021/11/30 14:23:36] 310395440 fragments to be searched in 1 slices (4.63 GB total) [2021/11/30 14:23:36] Operating on slice 1 of 1: [2021/11/30 14:23:42] Fragment index slice generated in 6.29 s [2021/11/30 14:23:49] 001. 08052021_sjr_0090.mzBIN 6.4 s | deisotoping 0.6 s [2021/11/30 14:23:51] [progress: 5037/5037 (100%) - 4694 spectra/s] 1.1s | postprocessing 0.9 s [2021/11/30 14:23:59] 002. 08052021_sjr_0091.mzBIN 6.3 s | deisotoping 1.1 s [2021/11/30 14:24:01] [progress: 16993/16993 (100%) - 9520 spectra/s] 1.8s | postprocessing 0.9 s [2021/11/30 14:24:03] 003. 08052021_sjr_0092.mzBIN 1.8 s | deisotoping 0.0 s [2021/11/30 14:24:04] [progress: 5783/5783 (100%) - 17631 spectra/s] 0.3s | postprocessing 0.4 s [2021/11/30 14:24:44] 004. 08052021_sjr_0093.mzBIN 37.3 s | deisotoping 2.9 s [2021/11/30 14:24:51] [progress: 55144/55144 (100%) - 14075 spectra/s] 3.9s | postprocessing 2.6 s [2021/11/30 14:24:56] 005. 08052021_sjr_0094.mzBIN 4.8 s | deisotoping 0.1 s [2021/11/30 14:24:58] [progress: 12840/12840 (100%) - 15053 spectra/s] 0.9s | postprocessing 0.8 s [2021/11/30 14:25:01] 006. 08052021_sjr_0095.mzBIN 2.8 s | deisotoping 0.1 s [2021/11/30 14:25:02] [progress: 8920/8920 (100%) - 15649 spectra/s] 0.6s | postprocessing 0.6 s [2021/11/30 14:25:04] 007. 08052021_sjr_0096.mzBIN 2.5 s | deisotoping 0.1 s [2021/11/30 14:25:05] [progress: 8255/8255 (100%) - 18977 spectra/s] 0.4s | postprocessing 0.6 s [2021/11/30 14:25:10] 008. 08052021_sjr_0097.mzBIN 4.5 s | deisotoping 0.2 s [2021/11/30 14:25:12] [progress: 12390/12390 (100%) - 16834 spectra/s] 0.7s | postprocessing 0.6 s [2021/11/30 14:25:18] 009. 08052021_sjr_0098.mzBIN 5.9 s | deisotoping 0.3 s [2021/11/30 14:25:20] [progress: 15515/15515 (100%) - 17772 spectra/s] 0.9s | postprocessing 0.8 s [2021/11/30 14:25:20] ***************************MAIN SEARCH DONE IN 2.657 MIN*************************** [2021/11/30 14:25:20] [2021/11/30 14:25:20] *******************************TOTAL TIME 2.754 MIN******************************** [2021/12/01 09:30:26] Search canceled.