Detecting decoy prefix in 2_site_library_23_02_08.fasta. No common prefixes were found. No common suffixes were found. No decoy prefix detected. A new FASTA will be generated using reverse sequences as decoys (with prefix 'DECOY_'). Using decoy database at decoy_2_site_library_23_02_08.fasta. MSFragger version MSFragger-3.4 Batmass-IO version 1.23.6 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.1, OpenJDK 64-Bit Server VM, Oracle Corporation JVM started with 16 GB memory Checking database... Checking spectral files... 12:27:55:940 [pool-1-thread-1] INFO PlatformDependent - Your platform does not provide complete low-level API for accessing direct buffers reliably. Unless explicitly requested, heap buffer will always be preferred to avoid potential system instability. C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_ACE_12p5.raw: Scans = 8426 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_ACE_25.raw: Scans = 9691 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_12p5.raw: Scans = 8834 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_25.raw: Scans = 9946 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_ACE_50.raw: Scans = 10736 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_ACE_100.raw: Scans = 12166 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_50.raw: Scans = 11374 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_100.raw: Scans = 12640 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_ACE_6p25.raw: Scans = 5795 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_6p25.raw: Scans = 6779 ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 12 database_name = C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\decoy_2_site_library_23_02_08.fasta decoy_prefix = DECOY_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 0 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = CNBr search_enzyme_sense_1 = C search_enzyme_cut_1 = M search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 0 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5500 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 5 digest_max_length = 60 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 50 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = -0.984016 cR 3 add_C_cysteine = 0 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 Number of unique peptides of length 14: 576 In total 576 peptides. Generated 864 modified peptides. Number of peptides with more than 5500 modification patterns: 0 Selected fragment index width 0.10 Da. 22464 fragments to be searched in 1 slices (0.00 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.03 s 001. 314_23_10_02_JSA485_100.raw 16.1 s | deisotoping 0.5 s [progress: 12211/12211 (100%) - 23083 spectra/s] 0.5s | postprocessing 0.5 s 002. 314_23_10_02_JSA485_12p5.raw 11.3 s | deisotoping 0.0 s [progress: 7411/7411 (100%) - 72657 spectra/s] 0.1s | postprocessing 0.2 s 003. 314_23_10_02_JSA485_25.raw 10.6 s | deisotoping 0.0 s [progress: 9470/9470 (100%) - 93762 spectra/s] 0.1s | postprocessing 0.2 s 004. 314_23_10_02_JSA485_50.raw 10.7 s | deisotoping 0.0 s [progress: 10966/10966 (100%) - 107510 spectra/s] 0.1s | postprocessing 0.2 s 005. 314_23_10_02_JSA485_6p25.raw 10.4 s | deisotoping 0.0 s [progress: 4771/4771 (100%) - 47710 spectra/s] 0.1s | postprocessing 0.1 s 006. 314_23_10_02_JSA485_ACE_100.raw 9.9 s | deisotoping 0.0 s [progress: 10789/10789 (100%) - 105775 spectra/s] 0.1s | postprocessing 0.2 s 007. 314_23_10_02_JSA485_ACE_12p5.raw 10.9 s | deisotoping 0.0 s [progress: 5496/5496 (100%) - 49964 spectra/s] 0.1s | postprocessing 0.0 s 008. 314_23_10_02_JSA485_ACE_25.raw 12.5 s | deisotoping 0.0 s [progress: 7459/7459 (100%) - 69065 spectra/s] 0.1s | postprocessing 0.1 s 009. 314_23_10_02_JSA485_ACE_50.raw 12.0 s | deisotoping 0.0 s [progress: 8975/8975 (100%) - 82339 spectra/s] 0.1s | postprocessing 0.1 s 010. 314_23_10_02_JSA485_ACE_6p25.raw 14.0 s | deisotoping 0.0 s [progress: 2233/2233 (100%) - 20676 spectra/s] 0.1s | postprocessing 0.0 s ***************************MAIN SEARCH DONE IN 2.040 MIN*************************** *******************************TOTAL TIME 2.266 MIN******************************** INFO: Writing results to output directory 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output'. INFO: CPU: DESKTOP-J8TBBGG INFO: Crux version: 4.1 INFO: Mon 02/13/2023 INFO: Beginning percolator. INFO: Percolator version 3.05.nightly-137-e806a0c5, Build Date Oct 8 2021 22:15:04 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 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.peptides.txt --decoy-results-peptides C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.peptides.txt --results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.psms.txt --decoy-results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_100.fixed.pin INFO: Started Mon Feb 13 12:30:15 2023 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_100.fixed.pin INFO: Features: INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7 INFO: Found 3044 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 3035 positives and 9 negatives, size ratio=337.222 and pi0=1 INFO: Warning : the number of negative samples read is too small to perform a correct classification. INFO: INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 1 as initial direction. Could separate 2022 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 1 as initial direction. Could separate 2024 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 1 as initial direction. Could separate 2024 training set positives with q<0.01 in that direction. INFO: Found 3035 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0450 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 3035 PSMs with q<0.05 INFO: Iteration 2: Estimated 3035 PSMs with q<0.05 INFO: Iteration 3: Estimated 3035 PSMs with q<0.05 INFO: Iteration 4: Estimated 3035 PSMs with q<0.05 INFO: Iteration 5: Estimated 3035 PSMs with q<0.05 INFO: Iteration 6: Estimated 3035 PSMs with q<0.05 INFO: Iteration 7: Estimated 3035 PSMs with q<0.05 INFO: Iteration 8: Estimated 3035 PSMs with q<0.05 INFO: Iteration 9: Estimated 3035 PSMs with q<0.05 INFO: Iteration 10: Estimated 3035 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.1951 0.4771 0.2091 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.3291 0.0111 -0.2446 abs_ppm INFO: 0.6539 0.7611 0.6980 isotope_errors INFO: -1.4310 -1.5763 -1.9949 log10_evalue INFO: 0.6376 -0.4195 -0.7742 hyperscore INFO: -0.1523 0.6313 -0.3804 delta_hyperscore INFO: -0.5454 0.4187 0.3437 matched_ion_num INFO: 0.3747 0.1447 0.1489 complementary_ions INFO: -0.6753 -0.7063 -0.2120 ion_series INFO: -0.3247 -0.3622 -0.0550 weighted_average_abs_fragment_ppm INFO: 0.0000 0.0000 0.0000 peptide_length INFO: 0.0000 0.0000 0.0000 ntt INFO: 0.0000 0.0000 0.0000 nmc INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.0762 0.0453 0.2004 Charge2 INFO: -0.1122 -0.1166 -0.0048 Charge3 INFO: 0.1665 0.0049 0.0237 Charge4 INFO: -0.2214 0.2026 -0.2438 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 2.8291 2.8330 2.6138 m0 INFO: Found 3035 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 3035 target PSMs and 9 decoy PSMs. INFO: Multiple instantiations of Normalizer INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. INFO: Calculating q values. INFO: Final list yields 292 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 13.2920 cpu seconds or 13 seconds wall clock time. INFO: Multiple instantiations of Normalizer WARNING: No modification identifier found for mass shift -0.98. Warning Suppressed, others may exist INFO: Creating modification for -0.984000 INFO: Elapsed time: 13.5 s INFO: Finished crux percolator. INFO: Return Code:0 WARNING: The output directory 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output' already exists. Existing files will be overwritten. WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.log.txt' already exists and will be overwritten. INFO: CPU: DESKTOP-J8TBBGG INFO: Crux version: 4.1 INFO: Mon 02/13/2023 INFO: Beginning percolator. INFO: Percolator version 3.05.nightly-137-e806a0c5, Build Date Oct 8 2021 22:15:04 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 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.peptides.txt --decoy-results-peptides C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.peptides.txt --results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.psms.txt --decoy-results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_12p5.fixed.pin INFO: Started Mon Feb 13 12:30:30 2023 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_12p5.fixed.pin INFO: Features: INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7 INFO: Found 1355 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 1353 positives and 2 negatives, size ratio=676.5 and pi0=1 INFO: Warning : the number of negative samples read is too small to perform a correct classification. INFO: INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 1 as initial direction. Could separate 901 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 1 as initial direction. Could separate 902 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 1 as initial direction. Could separate 903 training set positives with q<0.01 in that direction. INFO: Found 1353 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.1970 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 1353 PSMs with q<0.05 INFO: Iteration 2: Estimated 1353 PSMs with q<0.05 INFO: Iteration 3: Estimated 1353 PSMs with q<0.05 INFO: Iteration 4: Estimated 1353 PSMs with q<0.05 INFO: Iteration 5: Estimated 1353 PSMs with q<0.05 INFO: Iteration 6: Estimated 1353 PSMs with q<0.05 INFO: Iteration 7: Estimated 1353 PSMs with q<0.05 INFO: Iteration 8: Estimated 1353 PSMs with q<0.05 INFO: Iteration 9: Estimated 1353 PSMs with q<0.05 INFO: Iteration 10: Estimated 1353 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.7037 0.2561 0.2131 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.2406 -0.3445 0.0649 abs_ppm INFO: 0.4356 0.2290 0.2555 isotope_errors INFO: -0.2168 0.0782 -0.3143 log10_evalue INFO: 0.9068 0.5277 0.1249 hyperscore INFO: 0.2783 0.1555 0.0206 delta_hyperscore INFO: -0.6472 -0.3536 -0.2848 matched_ion_num INFO: 0.3032 0.3903 -0.1792 complementary_ions INFO: -0.5011 -0.3031 0.0501 ion_series INFO: -0.1711 0.4579 -0.3339 weighted_average_abs_fragment_ppm INFO: 0.0000 0.0000 0.0000 peptide_length INFO: 0.0000 0.0000 0.0000 ntt INFO: 0.0000 0.0000 0.0000 nmc INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.0000 0.0000 0.0000 Charge2 INFO: -0.0558 -0.1692 0.0161 Charge3 INFO: -0.1810 -0.1175 0.0035 Charge4 INFO: 0.3273 0.3671 -0.0237 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 1.9785 1.7040 1.5756 m0 INFO: Found 1353 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 1353 target PSMs and 2 decoy PSMs. INFO: Log transforming all scores prior to PEP calculation INFO: Multiple instantiations of Normalizer INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. INFO: Calculating q values. INFO: Final list yields 243 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Log transforming all scores prior to PEP calculation INFO: Processing took 4.5790 cpu seconds or 4 seconds wall clock time. INFO: Multiple instantiations of Normalizer WARNING: No modification identifier found for mass shift -0.98. Warning Suppressed, others may exist INFO: Creating modification for -0.984000 WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.pep.xml' already exists and will be overwritten. INFO: Elapsed time: 4.84 s INFO: Finished crux percolator. INFO: Return Code:0 WARNING: The output directory 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output' already exists. Existing files will be overwritten. WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.log.txt' already exists and will be overwritten. INFO: CPU: DESKTOP-J8TBBGG INFO: Crux version: 4.1 INFO: Mon 02/13/2023 INFO: Beginning percolator. INFO: Percolator version 3.05.nightly-137-e806a0c5, Build Date Oct 8 2021 22:15:04 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 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.peptides.txt --decoy-results-peptides C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.peptides.txt --results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.psms.txt --decoy-results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_25.fixed.pin INFO: Started Mon Feb 13 12:30:37 2023 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_25.fixed.pin INFO: Features: INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7 INFO: Found 2238 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 2229 positives and 9 negatives, size ratio=247.667 and pi0=1 INFO: Warning : the number of negative samples read is too small to perform a correct classification. INFO: INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 1 as initial direction. Could separate 1486 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 1 as initial direction. Could separate 1486 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 1 as initial direction. Could separate 1486 training set positives with q<0.01 in that direction. INFO: Found 2229 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.1300 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 2229 PSMs with q<0.05 INFO: Iteration 2: Estimated 2229 PSMs with q<0.05 INFO: Iteration 3: Estimated 2229 PSMs with q<0.05 INFO: Iteration 4: Estimated 2229 PSMs with q<0.05 INFO: Iteration 5: Estimated 2229 PSMs with q<0.05 INFO: Iteration 6: Estimated 2229 PSMs with q<0.05 INFO: Iteration 7: Estimated 2229 PSMs with q<0.05 INFO: Iteration 8: Estimated 2229 PSMs with q<0.05 INFO: Iteration 9: Estimated 2229 PSMs with q<0.05 INFO: Iteration 10: Estimated 2229 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -0.0470 0.0492 0.2415 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.5062 -0.4749 -0.5383 abs_ppm INFO: 0.3852 0.5468 0.4242 isotope_errors INFO: -0.1518 -0.1049 -0.3890 log10_evalue INFO: 1.5811 1.2921 0.5357 hyperscore INFO: 0.2729 0.0461 -0.1168 delta_hyperscore INFO: -0.7554 -0.2104 0.0222 matched_ion_num INFO: 0.3676 0.7760 0.6968 complementary_ions INFO: -0.7993 -0.8713 -0.4373 ion_series INFO: 0.2482 0.0286 0.1817 weighted_average_abs_fragment_ppm INFO: 0.0000 0.0000 0.0000 peptide_length INFO: 0.0000 0.0000 0.0000 ntt INFO: 0.0000 0.0000 0.0000 nmc INFO: 0.0000 0.0000 0.0000 Charge1 INFO: -0.0057 -0.0243 0.0126 Charge2 INFO: 0.2274 -0.2501 -0.2055 Charge3 INFO: -0.1859 0.0059 0.1802 Charge4 INFO: -0.0507 0.4580 0.0200 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 2.2447 2.4332 2.4101 m0 INFO: Found 2229 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 2229 target PSMs and 9 decoy PSMs. INFO: Multiple instantiations of Normalizer INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. INFO: Calculating q values. INFO: Final list yields 283 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 12.0050 cpu seconds or 12 seconds wall clock time. INFO: Multiple instantiations of Normalizer WARNING: No modification identifier found for mass shift -0.98. Warning Suppressed, others may exist INFO: Creating modification for -0.984000 WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.pep.xml' already exists and will be overwritten. INFO: Elapsed time: 12.2 s INFO: Finished crux percolator. INFO: Return Code:0 WARNING: The output directory 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output' already exists. Existing files will be overwritten. WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.log.txt' already exists and will be overwritten. INFO: CPU: DESKTOP-J8TBBGG INFO: Crux version: 4.1 INFO: Mon 02/13/2023 INFO: Beginning percolator. INFO: Percolator version 3.05.nightly-137-e806a0c5, Build Date Oct 8 2021 22:15:04 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 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.peptides.txt --decoy-results-peptides C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.peptides.txt --results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.psms.txt --decoy-results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_50.fixed.pin INFO: Started Mon Feb 13 12:30:52 2023 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_50.fixed.pin INFO: Features: INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7 INFO: Found 2816 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 2813 positives and 3 negatives, size ratio=937.667 and pi0=1 INFO: Warning : the number of negative samples read is too small to perform a correct classification. INFO: INFO: Selecting Cpos by cross-validation. INFO: Selecting Cneg by cross-validation. INFO: Split 1: Selected feature 1 as initial direction. Could separate 1876 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 1 as initial direction. Could separate 1874 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 1 as initial direction. Could separate 1876 training set positives with q<0.01 in that direction. INFO: Found 2813 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0380 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 2813 PSMs with q<0.05 INFO: Iteration 2: Estimated 2813 PSMs with q<0.05 INFO: Iteration 3: Estimated 2813 PSMs with q<0.05 INFO: Iteration 4: Estimated 2813 PSMs with q<0.05 INFO: Iteration 5: Estimated 2813 PSMs with q<0.05 INFO: Iteration 6: Estimated 2813 PSMs with q<0.05 INFO: Iteration 7: Estimated 2813 PSMs with q<0.05 INFO: Iteration 8: Estimated 2813 PSMs with q<0.05 INFO: Iteration 9: Estimated 2813 PSMs with q<0.05 INFO: Iteration 10: Estimated 2813 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.0766 0.1643 0.1747 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.2245 -0.2461 -0.2898 abs_ppm INFO: 0.3899 0.5645 0.5276 isotope_errors INFO: -0.2377 -0.2549 -0.2405 log10_evalue INFO: 0.2586 0.0309 0.0881 hyperscore INFO: -0.3219 -0.1292 -0.1315 delta_hyperscore INFO: -0.0806 0.1809 0.2207 matched_ion_num INFO: 0.5250 0.8544 0.7524 complementary_ions INFO: -0.2430 -0.3309 -0.4053 ion_series INFO: 0.0466 0.1840 0.2790 weighted_average_abs_fragment_ppm INFO: 0.0000 0.0000 0.0000 peptide_length INFO: 0.0000 0.0000 0.0000 ntt INFO: 0.0000 0.0000 0.0000 nmc INFO: 0.0000 0.0000 0.0000 Charge1 INFO: 0.0372 0.1009 -0.0768 Charge2 INFO: -0.3106 -0.3501 -0.3125 Charge3 INFO: 0.2392 0.2359 0.2528 Charge4 INFO: 0.1061 0.1616 0.1523 Charge5 INFO: 0.0046 -0.0005 0.0306 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 2.2196 2.3667 2.3442 m0 INFO: Found 2813 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 2813 target PSMs and 3 decoy PSMs. INFO: Multiple instantiations of Normalizer INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. INFO: Calculating q values. INFO: Final list yields 282 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Log transforming all scores prior to PEP calculation INFO: Processing took 12.5590 cpu seconds or 13 seconds wall clock time. INFO: Multiple instantiations of Normalizer WARNING: No modification identifier found for mass shift -0.98. Warning Suppressed, others may exist INFO: Creating modification for -0.984000 WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.pep.xml' already exists and will be overwritten. INFO: Elapsed time: 12.7 s INFO: Finished crux percolator. INFO: Return Code:0 WARNING: The output directory 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output' already exists. Existing files will be overwritten. WARNING: The file 'C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.log.txt' already exists and will be overwritten. INFO: CPU: DESKTOP-J8TBBGG INFO: Crux version: 4.1 INFO: Mon 02/13/2023 INFO: Beginning percolator. INFO: Percolator version 3.05.nightly-137-e806a0c5, Build Date Oct 8 2021 22:15:04 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 C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.peptides.txt --decoy-results-peptides C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.peptides.txt --results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.target.psms.txt --decoy-results-psms C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\crux-output/percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern DECOY_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.05 --maxiter 10 --search-input auto --no-schema-validation --protein-enzyme trypsin --post-processing-tdc C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_6p25.fixed.pin INFO: Started Mon Feb 13 12:31:06 2023 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile C:\Users\Owner\Desktop\Pentelute\LCMS_Data\314_Orbi_Start_22_11_21\314_23_02_10\314_23_10_02_JSA485_6p25.fixed.pin INFO: Features: INFO: retentiontime rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm peptide_length ntt nmc Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 Charge7 INFO: Found 501 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 501 positives and 0 negatives, size ratio=inf and pi0=1 FATAL: An exception occurred: Error: no decoy PSMs were provided. Search canceled.