anesvi
commented
4 years ago Are you running timsTOF data using PD? We only support Thermo data in PD . Maybe I am confused about ‘Bruker’ in the job name
At the moment we do not have time/resources to help with PD. I recommend you use FragPipe.
BEst Alexey
From: stharan notifications@github.com Sent: Monday, June 29, 2020 3:38 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Nesvilab/MSFragger] PD node Error: An item with the same key has already been added. (#81)
External Email - Use Caution
Hi,
I was able to do several searches with mgf files in PD. However, the last couple have given me this same error. Please see below for a part of the log file.
Best,
Tharan MagellanServer.loghttps://github.com/Nesvilab/MSFragger/files/4847655/MagellanServer.log
2020-06-29 14:59:58,677 DEBUG [43] JobManager - Adding job - set event. 2020-06-29 14:59:58,677 DEBUG [43] JobManager - JobQueue (2 jobs queued) WorkflowID, Creation Time, State, Name, Type, Owner 171, 06/29/2020 14:59:56, Running, 20191021_K562_200ng_90min_Slot1-1_01_4786_53113, P, (BrukerDemo) 172, 06/29/2020 14:59:58, Waiting, 20191021_K562_200ng_90min_Slot1-1_01_4786_53113, C, (BrukerDemo)
2020-06-29 15:00:00,876 DEBUG [46] SpectrumFilesNode - (171-0) Fire OnProcessingFinishedEvent. 2020-06-29 15:00:00,922 DEBUG [46] SpectrumSelectorNode - (171-16) Profile spectra are not sent. 2020-06-29 15:00:01,188 DEBUG [46] SpectrumSelectorNode - (171-16) Open file 1 of 1 F2: D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf 2020-06-29 15:00:37,812 DEBUG [46] SpectrumSelectorNode - (171-16) Reading from file 1 of 1 F2: D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf (293991 spectra total) 2020-06-29 15:00:42,653 INFO [46] MSFragger - (171-15) MSFragger version MSFragger-3.0 2020-06-29 15:00:42,675 INFO [46] MSFragger - (171-15) Batmass-IO version 1.17.4 2020-06-29 15:00:42,692 INFO [46] MSFragger - (171-15) (c) University of Michigan 2020-06-29 15:00:42,705 INFO [46] MSFragger - (171-15) RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. 2020-06-29 15:00:42,719 INFO [46] MSFragger - (171-15) System OS: Windows 10, Architecture: AMD64 2020-06-29 15:00:42,719 INFO [46] MSFragger - (171-15) Java Info: 1.8.0_251, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation 2020-06-29 15:00:42,748 INFO [46] MSFragger - (171-15) JVM started with 100 GB memory 2020-06-29 15:00:42,761 INFO [46] MSFragger - (171-15) Checking database... 2020-06-29 15:00:43,309 INFO [46] MSFragger - (171-15) Checking D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf... 2020-06-29 15:00:55,152 INFO [46] MSFragger - (171-15) FIRST SEARCH* 2020-06-29 15:00:55,173 INFO [46] MSFragger - (171-15) Parameters: 2020-06-29 15:00:55,190 INFO [46] MSFragger - (171-15) num_threads = 40 2020-06-29 15:00:55,207 INFO [46] MSFragger - (171-15) database_name = D:\200ng_K562\PD_4786_Fragger\temp171\Human_2020-05-05-R-C-UP000005640_combined.fasta 2020-06-29 15:00:55,223 INFO [46] MSFragger - (171-15) decoyprefix = rev 2020-06-29 15:00:55,242 INFO [46] MSFragger - (171-15) precursor_mass_lower = -20.0 2020-06-29 15:00:55,259 INFO [46] MSFragger - (171-15) precursor_mass_upper = 20.0 2020-06-29 15:00:55,277 INFO [46] MSFragger - (171-15) precursor_mass_units = 1 2020-06-29 15:00:55,293 INFO [46] MSFragger - (171-15) precursor_true_tolerance = 20.0 2020-06-29 15:00:55,309 INFO [46] MSFragger - (171-15) precursor_true_units = 1 2020-06-29 15:00:55,325 INFO [46] MSFragger - (171-15) fragment_mass_tolerance = 50.0 2020-06-29 15:00:55,341 INFO [46] MSFragger - (171-15) fragment_mass_units = 1 2020-06-29 15:00:55,358 INFO [46] MSFragger - (171-15) calibrate_mass = 2 2020-06-29 15:00:55,374 INFO [46] MSFragger - (171-15) write_calibrated_mgf = false 2020-06-29 15:00:55,374 INFO [46] MSFragger - (171-15) isotope_error = 0/1 2020-06-29 15:00:55,405 INFO [46] MSFragger - (171-15) mass_offsets = 0 2020-06-29 15:00:55,421 INFO [46] MSFragger - (171-15) labile_search_mode = OFF 2020-06-29 15:00:55,421 INFO [46] MSFragger - (171-15) precursor_mass_mode = SELECTED 2020-06-29 15:00:55,450 INFO [46] MSFragger - (171-15) localize_delta_mass = false 2020-06-29 15:00:55,467 INFO [46] MSFragger - (171-15) delta_mass_exclude_ranges = (-1.5,3.5) 2020-06-29 15:00:55,485 INFO [46] MSFragger - (171-15) fragment_ion_series = b,y 2020-06-29 15:00:55,568 INFO [46] MSFragger - (171-15) diagnostic_intensity_filter = 0.0 2020-06-29 15:00:55,610 INFO [46] MSFragger - (171-15) Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 2020-06-29 15:00:55,625 INFO [46] MSFragger - (171-15) diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 2020-06-29 15:00:55,641 INFO [46] MSFragger - (171-15) search_enzyme_name = Trypsin 2020-06-29 15:00:55,657 INFO [46] MSFragger - (171-15) search_enzyme_cutafter = KR 2020-06-29 15:00:55,674 INFO [46] MSFragger - (171-15) search_enzyme_butnotafter = P 2020-06-29 15:00:55,690 INFO [46] MSFragger - (171-15) num_enzyme_termini = 2 2020-06-29 15:00:55,706 INFO [46] MSFragger - (171-15) allowed_missed_cleavage = 1 2020-06-29 15:00:55,735 INFO [46] MSFragger - (171-15) clip_nTerm_M = true 2020-06-29 15:00:55,753 INFO [46] MSFragger - (171-15) allow_multiple_variable_mods_on_residue = false 2020-06-29 15:00:55,770 INFO [46] MSFragger - (171-15) max_variable_mods_per_peptide = 3 2020-06-29 15:00:55,787 INFO [46] MSFragger - (171-15) max_variable_mods_combinations = 5000 2020-06-29 15:00:55,805 INFO [46] MSFragger - (171-15) output_file_extension = pepXML 2020-06-29 15:00:55,822 INFO [46] MSFragger - (171-15) output_format = pepXML 2020-06-29 15:00:55,839 INFO [46] MSFragger - (171-15) output_report_topN = 1 2020-06-29 15:00:55,858 INFO [46] MSFragger - (171-15) output_max_expect = 50.0 2020-06-29 15:00:55,876 INFO [46] MSFragger - (171-15) report_alternative_proteins = false 2020-06-29 15:00:55,893 INFO [46] MSFragger - (171-15) override_charge = false 2020-06-29 15:00:55,910 INFO [46] MSFragger - (171-15) precursor_charge_low = 1 2020-06-29 15:00:55,927 INFO [46] MSFragger - (171-15) precursor_charge_high = 4 2020-06-29 15:00:55,945 INFO [46] MSFragger - (171-15) digest_min_length = 6 2020-06-29 15:00:55,962 INFO [46] MSFragger - (171-15) digest_max_length = 50 2020-06-29 15:00:55,980 INFO [46] MSFragger - (171-15) digest_mass_range_low = 500.0 2020-06-29 15:00:55,996 INFO [46] MSFragger - (171-15) digest_mass_range_high = 5000.0 2020-06-29 15:00:56,012 INFO [46] MSFragger - (171-15) max_fragment_charge = 2 2020-06-29 15:00:56,027 INFO [46] MSFragger - (171-15) deisotope = 1 2020-06-29 15:00:56,043 INFO [46] MSFragger - (171-15) track_zero_topN = 0 2020-06-29 15:00:56,058 INFO [46] MSFragger - (171-15) zero_bin_accept_expect = 0.0 2020-06-29 15:00:56,075 INFO [46] MSFragger - (171-15) zero_bin_mult_expect = 1.0 2020-06-29 15:00:56,098 INFO [46] MSFragger - (171-15) add_topN_complementary = 0 2020-06-29 15:00:56,150 INFO [46] MSFragger - (171-15) minimum_peaks = 15 2020-06-29 15:00:56,169 INFO [46] MSFragger - (171-15) use_topN_peaks = 150 2020-06-29 15:00:56,186 INFO [46] MSFragger - (171-15) minIonsScoring = 2 2020-06-29 15:00:56,202 INFO [46] MSFragger - (171-15) min_matched_fragments = 3 2020-06-29 15:00:56,230 INFO [46] MSFragger - (171-15) minimum_ratio = 0.01 2020-06-29 15:00:56,246 INFO [46] MSFragger - (171-15) intensity_transform = 0 2020-06-29 15:00:56,262 INFO [46] MSFragger - (171-15) remove_precursor_peak = 0 2020-06-29 15:00:56,278 INFO [46] MSFragger - (171-15) remove_precursor_range = -1.5,1.5 2020-06-29 15:00:56,294 INFO [46] MSFragger - (171-15) clear_mz_range_low = 0.0 2020-06-29 15:00:56,309 INFO [46] MSFragger - (171-15) clear_mz_range_high = 0.0 2020-06-29 15:00:56,325 INFO [46] MSFragger - (171-15) excluded_scan_list_file = 2020-06-29 15:00:56,343 INFO [46] MSFragger - (171-15) mass_diff_to_variable_mod = 0 2020-06-29 15:00:56,388 INFO [46] MSFragger - (171-15) variable_mod_01 = 15.994915 M 3 2020-06-29 15:00:56,404 INFO [46] MSFragger - (171-15) variable_mod_14 = 42.010565 [^ 3 2020-06-29 15:00:56,420 INFO [46] MSFragger - (171-15) add_C_cysteine = 57.021464 2020-06-29 15:00:56,437 INFO [46] MSFragger - (171-15) add_Cterm_peptide = 0.0 2020-06-29 15:00:56,454 INFO [46] MSFragger - (171-15) add_Cterm_protein = 0.0 2020-06-29 15:00:56,470 INFO [46] MSFragger - (171-15) add_Nterm_peptide = 0.0 2020-06-29 15:00:56,487 INFO [46] MSFragger - (171-15) add_Nterm_protein = 0.0 2020-06-29 15:00:56,769 INFO [46] MSFragger - (171-15) Number of unique peptides 2020-06-29 15:00:57,830 INFO [46] MSFragger - (171-15) of length 6: 212285 2020-06-29 15:00:57,852 INFO [46] MSFragger - (171-15) of length 7: 217633 2020-06-29 15:00:57,865 INFO [46] MSFragger - (171-15) of length 8: 201888 2020-06-29 15:00:57,878 INFO [46] MSFragger - (171-15) of length 9: 193753 2020-06-29 15:00:57,892 INFO [46] MSFragger - (171-15) of length 10: 177275 2020-06-29 15:00:57,892 INFO [46] MSFragger - (171-15) of length 11: 163085 2020-06-29 15:00:57,920 INFO [46] MSFragger - (171-15) of length 12: 150990 2020-06-29 15:00:57,933 INFO [46] MSFragger - (171-15) of length 13: 142741 2020-06-29 15:00:57,946 INFO [46] MSFragger - (171-15) of length 14: 128090 2020-06-29 15:00:57,959 INFO [46] MSFragger - (171-15) of length 15: 119912 2020-06-29 15:00:57,972 INFO [46] MSFragger - (171-15) of length 16: 109392 2020-06-29 15:00:57,987 INFO [46] MSFragger - (171-15) of length 17: 100142 2020-06-29 15:00:58,000 INFO [46] MSFragger - (171-15) of length 18: 93275 2020-06-29 15:00:58,017 INFO [46] MSFragger - (171-15) of length 19: 87569 2020-06-29 15:00:58,051 INFO [46] MSFragger - (171-15) of length 20: 79535 2020-06-29 15:00:58,067 INFO [46] MSFragger - (171-15) of length 21: 74378 2020-06-29 15:00:58,083 INFO [46] MSFragger - (171-15) of length 22: 68132 2020-06-29 15:00:58,099 INFO [46] MSFragger - (171-15) of length 23: 63255 2020-06-29 15:00:58,115 INFO [46] MSFragger - (171-15) of length 24: 59282 2020-06-29 15:00:58,130 INFO [46] MSFragger - (171-15) of length 25: 54941 2020-06-29 15:00:58,147 INFO [46] MSFragger - (171-15) of length 26: 50359 2020-06-29 15:00:58,164 INFO [46] MSFragger - (171-15) of length 27: 47784 2020-06-29 15:00:58,184 INFO [46] MSFragger - (171-15) of length 28: 44545 2020-06-29 15:00:58,200 INFO [46] MSFragger - (171-15) of length 29: 40944 2020-06-29 15:00:58,216 INFO [46] MSFragger - (171-15) of length 30: 38124 2020-06-29 15:00:58,232 INFO [46] MSFragger - (171-15) of length 31: 35163 2020-06-29 15:00:58,248 INFO [46] MSFragger - (171-15) of length 32: 32893 2020-06-29 15:00:58,264 INFO [46] MSFragger - (171-15) of length 33: 30232 2020-06-29 15:00:58,279 INFO [46] MSFragger - (171-15) of length 34: 27907 2020-06-29 15:00:58,302 INFO [46] MSFragger - (171-15) of length 35: 25405 2020-06-29 15:00:58,359 INFO [46] MSFragger - (171-15) of length 36: 24278 2020-06-29 15:00:58,432 INFO [46] MSFragger - (171-15) of length 37: 21517 2020-06-29 15:00:58,466 INFO [46] MSFragger - (171-15) of length 38: 20129 2020-06-29 15:00:58,514 INFO [46] MSFragger - (171-15) of length 39: 17931 2020-06-29 15:00:58,533 INFO [46] MSFragger - (171-15) of length 40: 17085 2020-06-29 15:00:58,549 INFO [46] MSFragger - (171-15) of length 41: 16075 2020-06-29 15:00:58,567 INFO [46] MSFragger - (171-15) of length 42: 14285 2020-06-29 15:00:58,583 INFO [46] MSFragger - (171-15) of length 43: 12514 2020-06-29 15:00:58,599 INFO [46] MSFragger - (171-15) of length 44: 10069 2020-06-29 15:00:58,616 INFO [46] MSFragger - (171-15) of length 45: 7890 2020-06-29 15:00:58,633 INFO [46] MSFragger - (171-15) of length 46: 5324 2020-06-29 15:00:58,651 INFO [46] MSFragger - (171-15) of length 47: 3472 2020-06-29 15:00:58,667 INFO [46] MSFragger - (171-15) of length 48: 2131 2020-06-29 15:00:58,683 INFO [46] MSFragger - (171-15) of length 49: 1118 2020-06-29 15:00:58,699 INFO [46] MSFragger - (171-15) of length 50: 702 2020-06-29 15:00:58,714 INFO [46] MSFragger - (171-15) In total 3045429 peptides. 2020-06-29 15:00:58,752 INFO [46] MSFragger - (171-15) Generated 4550203 modified peptides. 2020-06-29 15:00:58,768 INFO [46] MSFragger - (171-15) Number of peptides with more than 5000 modification patterns: 0 2020-06-29 15:01:00,421 INFO [46] MSFragger - (171-15) Selected fragment tolerance 0.25 Da. 2020-06-29 15:01:00,506 INFO [46] MSFragger - (171-15) 162270300 fragments to be searched in 1 slices (2.42 GB total) 2020-06-29 15:01:00,524 INFO [46] MSFragger - (171-15) Operating on slice 1 of 1: 2020-06-29 15:01:01,798 INFO [46] MSFragger - (171-15) Fragment index slice generated in 1.29 s 2020-06-29 15:01:21,271 INFO [46] MSFragger - (171-15) 001. 20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf 18.0 s | deisotoping 1.5 s 2020-06-29 15:01:30,870 INFO [46] MSFragger - (171-15) [progress: 293990/293990 (100%) - 40284 spectra/s] 7.3s | postprocessing 1.4 s 2020-06-29 15:01:31,531 INFO [46] MSFragger - (171-15) FIRST SEARCH DONE IN 0.815 MIN 2020-06-29 15:01:31,550 INFO [46] MSFragger - (171-15) MASS CALIBRATION 2020-06-29 15:01:31,566 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:31,582 INFO [46] MSFragger - (171-15) | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) 2020-06-29 15:01:31,597 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:31,614 INFO [46] MSFragger - (171-15) Run | Median MAD | Median MAD | Median MAD | Median MAD 2020-06-29 15:01:48,876 INFO [46] MSFragger - (171-15) 001 | 2.07 4.01 | 0.13 3.31 | -2.02 6.34 | -1.36 6.38 2020-06-29 15:01:48,899 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:48,914 INFO [46] MSFragger - (171-15) Finding the optimal parameters: 2020-06-29 15:01:48,929 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:01:48,947 INFO [46] MSFragger - (171-15) MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 2020-06-29 15:01:48,963 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,371 INFO [46] MSFragger - (171-15) Count | 117029| 126087| 131713| 134096| 133026| skip rest 2020-06-29 15:02:53,395 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,414 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,432 INFO [46] MSFragger - (171-15) Peaks | 500_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 2020-06-29 15:02:53,451 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:03:44,335 INFO [46] MSFragger - (171-15) Count | 135126| 135126| 135126| 134096| skip rest 2020-06-29 15:03:44,360 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:03:44,378 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:44,395 INFO [46] MSFragger - (171-15) Int. | 1 2020-06-29 15:03:44,423 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,343 INFO [46] MSFragger - (171-15) Count | 136626 2020-06-29 15:03:57,369 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,387 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,405 INFO [46] MSFragger - (171-15) Rm P. | 1 2020-06-29 15:03:57,424 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:04:10,193 INFO [46] MSFragger - (171-15) Count | 136666 2020-06-29 15:04:10,213 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:04:10,232 INFO [46] MSFragger - (171-15) New fragment_mass_tolerance = 15 PPM 2020-06-29 15:04:10,250 INFO [46] MSFragger - (171-15) New use_topN_peaks = 175 2020-06-29 15:04:10,269 INFO [46] MSFragger - (171-15) New minimum_ratio = 0.000000 2020-06-29 15:04:10,288 INFO [46] MSFragger - (171-15) New intensity_transform = 1 2020-06-29 15:04:10,310 INFO [46] MSFragger - (171-15) New remove_precursor_peak = 1 2020-06-29 15:04:10,328 INFO [46] MSFragger - (171-15) **MASS CALIBRATION DONE IN 2.644 MIN 2020-06-29 15:04:10,347 INFO [46] MSFragger - (171-15) MAIN SEARCH 2020-06-29 15:04:10,366 INFO [46] MSFragger - (171-15) Checking database... 2020-06-29 15:04:10,383 INFO [46] MSFragger - (171-15) Parameters: 2020-06-29 15:04:10,401 INFO [46] MSFragger - (171-15) num_threads = 40 2020-06-29 15:04:10,418 INFO [46] MSFragger - (171-15) database_name = D:\200ng_K562\PD_4786_Fragger\temp171\Human_2020-05-05-R-C-UP000005640_combined.fasta 2020-06-29 15:04:10,437 INFO [46] MSFragger - (171-15) decoyprefix = rev 2020-06-29 15:04:10,454 INFO [46] MSFragger - (171-15) precursor_mass_lower = -50.0 2020-06-29 15:04:10,471 INFO [46] MSFragger - (171-15) precursor_mass_upper = 50.0 2020-06-29 15:04:10,488 INFO [46] MSFragger - (171-15) precursor_mass_units = 1 2020-06-29 15:04:10,504 INFO [46] MSFragger - (171-15) precursor_true_tolerance = 20.0 2020-06-29 15:04:10,521 INFO [46] MSFragger - (171-15) precursor_true_units = 1 2020-06-29 15:04:10,538 INFO [46] MSFragger - (171-15) fragment_mass_tolerance = 15.0 2020-06-29 15:04:10,558 INFO [46] MSFragger - (171-15) fragment_mass_units = 1 2020-06-29 15:04:10,575 INFO [46] MSFragger - (171-15) calibrate_mass = 2 2020-06-29 15:04:10,592 INFO [46] MSFragger - (171-15) write_calibrated_mgf = false 2020-06-29 15:04:10,617 INFO [46] MSFragger - (171-15) isotope_error = 0/1/2 2020-06-29 15:04:10,644 INFO [46] MSFragger - (171-15) mass_offsets = 0 2020-06-29 15:04:10,668 INFO [46] MSFragger - (171-15) labile_search_mode = OFF 2020-06-29 15:04:10,688 INFO [46] MSFragger - (171-15) precursor_mass_mode = SELECTED 2020-06-29 15:04:10,705 INFO [46] MSFragger - (171-15) localize_delta_mass = false 2020-06-29 15:04:10,740 INFO [46] MSFragger - (171-15) delta_mass_exclude_ranges = (-1.5,3.5) 2020-06-29 15:04:10,753 INFO [46] MSFragger - (171-15) fragment_ion_series = b,y 2020-06-29 15:04:10,776 INFO [46] MSFragger - (171-15) diagnostic_intensity_filter = 0.0 2020-06-29 15:04:10,794 INFO [46] MSFragger - (171-15) Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 2020-06-29 15:04:10,811 INFO [46] MSFragger - (171-15) diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 2020-06-29 15:04:10,827 INFO [46] MSFragger - (171-15) search_enzyme_name = Trypsin 2020-06-29 15:04:10,840 INFO [46] MSFragger - (171-15) search_enzyme_cutafter = KR 2020-06-29 15:04:10,861 INFO [46] MSFragger - (171-15) search_enzyme_butnotafter = P 2020-06-29 15:04:10,878 INFO [46] MSFragger - (171-15) num_enzyme_termini = 2 2020-06-29 15:04:10,895 INFO [46] MSFragger - (171-15) allowed_missed_cleavage = 2 2020-06-29 15:04:10,916 INFO [46] MSFragger - (171-15) clip_nTerm_M = true 2020-06-29 15:04:10,950 INFO [46] MSFragger - (171-15) allow_multiple_variable_mods_on_residue = true 2020-06-29 15:04:10,967 INFO [46] MSFragger - (171-15) max_variable_mods_per_peptide = 3 2020-06-29 15:04:10,986 INFO [46] MSFragger - (171-15) max_variable_mods_combinations = 5000 2020-06-29 15:04:11,005 INFO [46] MSFragger - (171-15) output_file_extension = pepXML 2020-06-29 15:04:11,023 INFO [46] MSFragger - (171-15) output_format = pepXML 2020-06-29 15:04:11,043 INFO [46] MSFragger - (171-15) output_report_topN = 1 2020-06-29 15:04:11,061 INFO [46] MSFragger - (171-15) output_max_expect = 50.0 2020-06-29 15:04:11,079 INFO [46] MSFragger - (171-15) report_alternative_proteins = true 2020-06-29 15:04:11,097 INFO [46] MSFragger - (171-15) override_charge = false 2020-06-29 15:04:11,114 INFO [46] MSFragger - (171-15) precursor_charge_low = 1 2020-06-29 15:04:11,132 INFO [46] MSFragger - (171-15) precursor_charge_high = 4 2020-06-29 15:04:11,150 INFO [46] MSFragger - (171-15) digest_min_length = 6 2020-06-29 15:04:11,170 INFO [46] MSFragger - (171-15) digest_max_length = 50 2020-06-29 15:04:11,188 INFO [46] MSFragger - (171-15) digest_mass_range_low = 500.0 2020-06-29 15:04:11,206 INFO [46] MSFragger - (171-15) digest_mass_range_high = 5000.0 2020-06-29 15:04:11,224 INFO [46] MSFragger - (171-15) max_fragment_charge = 2 2020-06-29 15:04:11,241 INFO [46] MSFragger - (171-15) deisotope = 1 2020-06-29 15:04:11,259 INFO [46] MSFragger - (171-15) track_zero_topN = 0 2020-06-29 15:04:11,280 INFO [46] MSFragger - (171-15) zero_bin_accept_expect = 0.0 2020-06-29 15:04:11,298 INFO [46] MSFragger - (171-15) zero_bin_mult_expect = 1.0 2020-06-29 15:04:11,316 INFO [46] MSFragger - (171-15) add_topN_complementary = 0 2020-06-29 15:04:11,334 INFO [46] MSFragger - (171-15) minimum_peaks = 15 2020-06-29 15:04:11,351 INFO [46] MSFragger - (171-15) use_topN_peaks = 175 2020-06-29 15:04:11,369 INFO [46] MSFragger - (171-15) minIonsScoring = 2 2020-06-29 15:04:11,386 INFO [46] MSFragger - (171-15) min_matched_fragments = 3 2020-06-29 15:04:11,406 INFO [46] MSFragger - (171-15) minimum_ratio = 0.0 2020-06-29 15:04:11,424 INFO [46] MSFragger - (171-15) intensity_transform = 1 2020-06-29 15:04:11,443 INFO [46] MSFragger - (171-15) remove_precursor_peak = 1 2020-06-29 15:04:11,461 INFO [46] MSFragger - (171-15) remove_precursor_range = -1.5,1.5 2020-06-29 15:04:11,480 INFO [46] MSFragger - (171-15) clear_mz_range_low = 0.0 2020-06-29 15:04:11,499 INFO [46] MSFragger - (171-15) clear_mz_range_high = 0.0 2020-06-29 15:04:11,517 INFO [46] MSFragger - (171-15) excluded_scan_list_file = 2020-06-29 15:04:11,537 INFO [46] MSFragger - (171-15) mass_diff_to_variable_mod = 0 2020-06-29 15:04:11,554 INFO [46] MSFragger - (171-15) variable_mod_01 = 15.994915 M 3 2020-06-29 15:04:11,572 INFO [46] MSFragger - (171-15) variable_mod_02 = 0.984016 NQ 3 2020-06-29 15:04:11,591 INFO [46] MSFragger - (171-15) variable_mod_14 = 42.010565 [^ 3 2020-06-29 15:04:11,609 INFO [46] MSFragger - (171-15) add_C_cysteine = 57.021464 2020-06-29 15:04:11,626 INFO [46] MSFragger - (171-15) add_Cterm_peptide = 0.0 2020-06-29 15:04:11,646 INFO [46] MSFragger - (171-15) add_Cterm_protein = 0.0 2020-06-29 15:04:11,663 INFO [46] MSFragger - (171-15) add_Nterm_peptide = 0.0 2020-06-29 15:04:11,682 INFO [46] MSFragger - (171-15) add_Nterm_protein = 0.0 2020-06-29 15:04:11,700 INFO [46] MSFragger - (171-15) Number of unique peptides 2020-06-29 15:04:12,278 INFO [46] MSFragger - (171-15) of length 6: 244659 2020-06-29 15:04:12,297 INFO [46] MSFragger - (171-15) of length 7: 262418 2020-06-29 15:04:12,314 INFO [46] MSFragger - (171-15) of length 8: 253525 2020-06-29 15:04:12,332 INFO [46] MSFragger - (171-15) of length 9: 251178 2020-06-29 15:04:12,349 INFO [46] MSFragger - (171-15) of length 10: 238922 2020-06-29 15:04:12,366 INFO [46] MSFragger - (171-15) of length 11: 227508 2020-06-29 15:04:12,385 INFO [46] MSFragger - (171-15) of length 12: 217702 2020-06-29 15:04:12,402 INFO [46] MSFragger - (171-15) of length 13: 213375 2020-06-29 15:04:12,420 INFO [46] MSFragger - (171-15) of length 14: 198654 2020-06-29 15:04:12,437 INFO [46] MSFragger - (171-15) of length 15: 190687 2020-06-29 15:04:12,454 INFO [46] MSFragger - (171-15) of length 16: 178542 2020-06-29 15:04:12,471 INFO [46] MSFragger - (171-15) of length 17: 168048 2020-06-29 15:04:12,488 INFO [46] MSFragger - (171-15) of length 18: 162390 2020-06-29 15:04:12,507 INFO [46] MSFragger - (171-15) of length 19: 157944 2020-06-29 15:04:12,525 INFO [46] MSFragger - (171-15) of length 20: 144011 2020-06-29 15:04:12,543 INFO [46] MSFragger - (171-15) of length 21: 137909 2020-06-29 15:04:12,560 INFO [46] MSFragger - (171-15) of length 22: 129721 2020-06-29 15:04:12,577 INFO [46] MSFragger - (171-15) of length 23: 121623 2020-06-29 15:04:12,594 INFO [46] MSFragger - (171-15) of length 24: 116623 2020-06-29 15:04:12,611 INFO [46] MSFragger - (171-15) of length 25: 109515 2020-06-29 15:04:12,629 INFO [46] MSFragger - (171-15) of length 26: 102416 2020-06-29 15:04:12,646 INFO [46] MSFragger - (171-15) of length 27: 97732 2020-06-29 15:04:12,663 INFO [46] MSFragger - (171-15) of length 28: 95936 2020-06-29 15:04:12,680 INFO [46] MSFragger - (171-15) of length 29: 85854 2020-06-29 15:04:12,697 INFO [46] MSFragger - (171-15) of length 30: 81437 2020-06-29 15:04:12,713 INFO [46] MSFragger - (171-15) of length 31: 77251 2020-06-29 15:04:12,731 INFO [46] MSFragger - (171-15) of length 32: 73282 2020-06-29 15:04:12,750 INFO [46] MSFragger - (171-15) of length 33: 68739 2020-06-29 15:04:12,768 INFO [46] MSFragger - (171-15) of length 34: 64540 2020-06-29 15:04:12,786 INFO [46] MSFragger - (171-15) of length 35: 58977 2020-06-29 15:04:12,803 INFO [46] MSFragger - (171-15) of length 36: 57757 2020-06-29 15:04:12,821 INFO [46] MSFragger - (171-15) of length 37: 53103 2020-06-29 15:04:12,838 INFO [46] MSFragger - (171-15) of length 38: 49710 2020-06-29 15:04:12,855 INFO [46] MSFragger - (171-15) of length 39: 45022 2020-06-29 15:04:12,875 INFO [46] MSFragger - (171-15) of length 40: 43118 2020-06-29 15:04:12,892 INFO [46] MSFragger - (171-15) of length 41: 40552 2020-06-29 15:04:12,908 INFO [46] MSFragger - (171-15) of length 42: 36967 2020-06-29 15:04:12,925 INFO [46] MSFragger - (171-15) of length 43: 31840 2020-06-29 15:04:12,942 INFO [46] MSFragger - (171-15) of length 44: 25446 2020-06-29 15:04:12,958 INFO [46] MSFragger - (171-15) of length 45: 19263 2020-06-29 15:04:12,975 INFO [46] MSFragger - (171-15) of length 46: 12575 2020-06-29 15:04:12,994 INFO [46] MSFragger - (171-15) of length 47: 7828 2020-06-29 15:04:13,011 INFO [46] MSFragger - (171-15) of length 48: 4572 2020-06-29 15:04:13,028 INFO [46] MSFragger - (171-15) of length 49: 2342 2020-06-29 15:04:13,046 INFO [46] MSFragger - (171-15) of length 50: 1366 2020-06-29 15:04:13,086 INFO [46] MSFragger - (171-15) In total 4962579 peptides. 2020-06-29 15:04:14,589 INFO [46] MSFragger - (171-15) Generated 42341316 modified peptides. 2020-06-29 15:04:14,607 INFO [46] MSFragger - (171-15) Number of peptides with more than 5000 modification patterns: 0 2020-06-29 15:04:19,430 INFO [46] MSFragger - (171-15) Selected fragment tolerance 0.08 Da. 2020-06-29 15:04:20,300 INFO [46] MSFragger - (171-15) 2267595348 fragments to be searched in 1 slices (33.79 GB total) 2020-06-29 15:04:20,322 INFO [46] MSFragger - (171-15) Operating on slice 1 of 1: 2020-06-29 15:04:42,729 INFO [46] MSFragger - (171-15) Fragment index slice generated in 22.43 s 2020-06-29 15:04:49,108 INFO [46] MSFragger - (171-15) 001. 20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mzBIN_calibrated 6.4 s 2020-06-29 15:05:07,440 INFO [46] MSFragger - (171-15) [progress: 87913/292598 (30%) - 8440 spectra/s] 2020-06-29 15:05:30,307 INFO [46] MSFragger - (171-15) [progress: 292598/292598 (100%) - 15961 spectra/s] 18.3s | postprocessing 22.3 s 2020-06-29 15:05:30,850 INFO [46] MSFragger - (171-15) MAIN SEARCH DONE IN 1.344 MIN 2020-06-29 15:05:30,871 INFO [46] MSFragger - (171-15) TOTAL TIME 4.803 MIN 2020-06-29 15:05:38,821 INFO [46] MSFragger - (171-15) MSFragger Running Time --0:4:59 2020-06-29 15:05:38,846 ERROR [46] MSFragger - (171-15) Error: An item with the same key has already been added. 2020-06-29 15:05:38,899 ERROR [46] MSFragger - (171-15) Could not process spectra due to following exception: An item with the same key has already been added. 2020-06-29 15:05:38,966 ERROR [46] JobManager+b - Exception caught -> Processing of Job (ID: 171) fails. System.ArgumentException: An item with the same key has already been added. at System.ThrowHelper.ThrowArgumentException(ExceptionResource resource) at System.Collections.Generic.Dictionary2.Insert(TKey key, TValue value, Boolean add) at MSFraggerPDv24.MSFragger.OnSpectraSentForSearch(IProcessingNode sender, MassSpectrumCollection spectraSent) at Thermo.Magellan.BL.Processing.PeptideAndProteinIdentificationNode.OnResultsSent(IProcessingNode sender, MassSpectrumCollection spectra) at Thermo.Magellan.BL.Processing.ProcessingNodeBase3.SendResults(TResult1 result) at Thermo.Magellan.RetrieverNodes.SpectrumSelectorNode.h() at Thermo.Magellan.RetrieverNodes.SpectrumSelectorNode.OnAllParentNodesFinished() at Thermo.Magellan.BL.Processing.ProcessingNodeBase.FireProcessingFinishedEvent(ResultsArguments eventArgs) at Thermo.Magellan.RetrieverNodes.SpectrumFilesNode.Process() at Thermo.Magellan.BL.Jobs.ProcessingJob.ExecuteNodesIncludingPostProcessingNodes(Action doExecuteNodes, Stopwatch timer) at Thermo.Magellan.BL.Jobs.CompositeJob.ExecuteChildJobs() at Thermo.Magellan.Services.JobManager.b.b() 2020-06-29 15:05:38,983 INFO [46] DataAccessBase - Removing Scratch file: D:\200ng_K562\PD_4786_Fragger\20191021_K562_200ng_90min_Slot1-1_01_4786_53113-(3).msf.scratch. 2020-06-29 15:05:39,013 DEBUG [46] ReportFile - Closing file [171]: D:\200ng_K562\PD_4786_Fragger\20191021_K562_200ng_90min_Slot1-1_01_4786_53113-(3).msf 2020-06-29 15:05:39,024 DEBUG [46] JobManager - JobQueue (2 jobs queued)
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stharan
huiyinc
Hi,
I was able to do several searches with mgf files in PD. However, the last couple have given me this same error. Please see below for a part of the log file.
Best,
Tharan MagellanServer.log
2020-06-29 14:59:58,677 DEBUG [43] JobManager - Adding job - set event. 2020-06-29 14:59:58,677 DEBUG [43] JobManager - JobQueue (2 jobs queued)
WorkflowID, Creation Time, State, Name, Type, Owner 171, 06/29/2020 14:59:56, Running, 20191021_K562_200ng_90min_Slot1-1_01_4786_53113, P, (BrukerDemo) 172, 06/29/2020 14:59:58, Waiting, 20191021_K562_200ng_90min_Slot1-1_01_4786_53113, C, (BrukerDemo)
2020-06-29 15:00:00,876 DEBUG [46] SpectrumFilesNode - (171-0) Fire OnProcessingFinishedEvent. 2020-06-29 15:00:00,922 DEBUG [46] SpectrumSelectorNode - (171-16) Profile spectra are not sent. 2020-06-29 15:00:01,188 DEBUG [46] SpectrumSelectorNode - (171-16) Open file 1 of 1 F2: D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf 2020-06-29 15:00:37,812 DEBUG [46] SpectrumSelectorNode - (171-16) Reading from file 1 of 1 F2: D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf (293991 spectra total) 2020-06-29 15:00:42,653 INFO [46] MSFragger - (171-15) MSFragger version MSFragger-3.0 2020-06-29 15:00:42,675 INFO [46] MSFragger - (171-15) Batmass-IO version 1.17.4 2020-06-29 15:00:42,692 INFO [46] MSFragger - (171-15) (c) University of Michigan 2020-06-29 15:00:42,705 INFO [46] MSFragger - (171-15) RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. 2020-06-29 15:00:42,719 INFO [46] MSFragger - (171-15) System OS: Windows 10, Architecture: AMD64 2020-06-29 15:00:42,719 INFO [46] MSFragger - (171-15) Java Info: 1.8.0_251, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation 2020-06-29 15:00:42,748 INFO [46] MSFragger - (171-15) JVM started with 100 GB memory 2020-06-29 15:00:42,761 INFO [46] MSFragger - (171-15) Checking database... 2020-06-29 15:00:43,309 INFO [46] MSFragger - (171-15) Checking D:\200ng_K562\20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf... 2020-06-29 15:00:55,152 INFO [46] MSFragger - (171-15) *****FIRST SEARCH**** 2020-06-29 15:00:55,173 INFO [46] MSFragger - (171-15) Parameters: 2020-06-29 15:00:55,190 INFO [46] MSFragger - (171-15) num_threads = 40 2020-06-29 15:00:55,207 INFO [46] MSFragger - (171-15) database_name = D:\200ng_K562\PD_4786_Fragger\temp171\Human_2020-05-05-R-C-UP000005640_combined.fasta 2020-06-29 15:00:55,223 INFO [46] MSFragger - (171-15) decoyprefix = rev 2020-06-29 15:00:55,242 INFO [46] MSFragger - (171-15) precursor_mass_lower = -20.0 2020-06-29 15:00:55,259 INFO [46] MSFragger - (171-15) precursor_mass_upper = 20.0 2020-06-29 15:00:55,277 INFO [46] MSFragger - (171-15) precursor_mass_units = 1 2020-06-29 15:00:55,293 INFO [46] MSFragger - (171-15) precursor_true_tolerance = 20.0 2020-06-29 15:00:55,309 INFO [46] MSFragger - (171-15) precursor_true_units = 1 2020-06-29 15:00:55,325 INFO [46] MSFragger - (171-15) fragment_mass_tolerance = 50.0 2020-06-29 15:00:55,341 INFO [46] MSFragger - (171-15) fragment_mass_units = 1 2020-06-29 15:00:55,358 INFO [46] MSFragger - (171-15) calibrate_mass = 2 2020-06-29 15:00:55,374 INFO [46] MSFragger - (171-15) write_calibrated_mgf = false 2020-06-29 15:00:55,374 INFO [46] MSFragger - (171-15) isotope_error = 0/1 2020-06-29 15:00:55,405 INFO [46] MSFragger - (171-15) mass_offsets = 0 2020-06-29 15:00:55,421 INFO [46] MSFragger - (171-15) labile_search_mode = OFF 2020-06-29 15:00:55,421 INFO [46] MSFragger - (171-15) precursor_mass_mode = SELECTED 2020-06-29 15:00:55,450 INFO [46] MSFragger - (171-15) localize_delta_mass = false 2020-06-29 15:00:55,467 INFO [46] MSFragger - (171-15) delta_mass_exclude_ranges = (-1.5,3.5) 2020-06-29 15:00:55,485 INFO [46] MSFragger - (171-15) fragment_ion_series = b,y 2020-06-29 15:00:55,568 INFO [46] MSFragger - (171-15) diagnostic_intensity_filter = 0.0 2020-06-29 15:00:55,610 INFO [46] MSFragger - (171-15) Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 2020-06-29 15:00:55,625 INFO [46] MSFragger - (171-15) diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 2020-06-29 15:00:55,641 INFO [46] MSFragger - (171-15) search_enzyme_name = Trypsin 2020-06-29 15:00:55,657 INFO [46] MSFragger - (171-15) search_enzyme_cutafter = KR 2020-06-29 15:00:55,674 INFO [46] MSFragger - (171-15) search_enzyme_butnotafter = P 2020-06-29 15:00:55,690 INFO [46] MSFragger - (171-15) num_enzyme_termini = 2 2020-06-29 15:00:55,706 INFO [46] MSFragger - (171-15) allowed_missed_cleavage = 1 2020-06-29 15:00:55,735 INFO [46] MSFragger - (171-15) clip_nTerm_M = true 2020-06-29 15:00:55,753 INFO [46] MSFragger - (171-15) allow_multiple_variable_mods_on_residue = false 2020-06-29 15:00:55,770 INFO [46] MSFragger - (171-15) max_variable_mods_per_peptide = 3 2020-06-29 15:00:55,787 INFO [46] MSFragger - (171-15) max_variable_mods_combinations = 5000 2020-06-29 15:00:55,805 INFO [46] MSFragger - (171-15) output_file_extension = pepXML 2020-06-29 15:00:55,822 INFO [46] MSFragger - (171-15) output_format = pepXML 2020-06-29 15:00:55,839 INFO [46] MSFragger - (171-15) output_report_topN = 1 2020-06-29 15:00:55,858 INFO [46] MSFragger - (171-15) output_max_expect = 50.0 2020-06-29 15:00:55,876 INFO [46] MSFragger - (171-15) report_alternative_proteins = false 2020-06-29 15:00:55,893 INFO [46] MSFragger - (171-15) override_charge = false 2020-06-29 15:00:55,910 INFO [46] MSFragger - (171-15) precursor_charge_low = 1 2020-06-29 15:00:55,927 INFO [46] MSFragger - (171-15) precursor_charge_high = 4 2020-06-29 15:00:55,945 INFO [46] MSFragger - (171-15) digest_min_length = 6 2020-06-29 15:00:55,962 INFO [46] MSFragger - (171-15) digest_max_length = 50 2020-06-29 15:00:55,980 INFO [46] MSFragger - (171-15) digest_mass_range_low = 500.0 2020-06-29 15:00:55,996 INFO [46] MSFragger - (171-15) digest_mass_range_high = 5000.0 2020-06-29 15:00:56,012 INFO [46] MSFragger - (171-15) max_fragment_charge = 2 2020-06-29 15:00:56,027 INFO [46] MSFragger - (171-15) deisotope = 1 2020-06-29 15:00:56,043 INFO [46] MSFragger - (171-15) track_zero_topN = 0 2020-06-29 15:00:56,058 INFO [46] MSFragger - (171-15) zero_bin_accept_expect = 0.0 2020-06-29 15:00:56,075 INFO [46] MSFragger - (171-15) zero_bin_mult_expect = 1.0 2020-06-29 15:00:56,098 INFO [46] MSFragger - (171-15) add_topN_complementary = 0 2020-06-29 15:00:56,150 INFO [46] MSFragger - (171-15) minimum_peaks = 15 2020-06-29 15:00:56,169 INFO [46] MSFragger - (171-15) use_topN_peaks = 150 2020-06-29 15:00:56,186 INFO [46] MSFragger - (171-15) minIonsScoring = 2 2020-06-29 15:00:56,202 INFO [46] MSFragger - (171-15) min_matched_fragments = 3 2020-06-29 15:00:56,230 INFO [46] MSFragger - (171-15) minimum_ratio = 0.01 2020-06-29 15:00:56,246 INFO [46] MSFragger - (171-15) intensity_transform = 0 2020-06-29 15:00:56,262 INFO [46] MSFragger - (171-15) remove_precursor_peak = 0 2020-06-29 15:00:56,278 INFO [46] MSFragger - (171-15) remove_precursor_range = -1.5,1.5 2020-06-29 15:00:56,294 INFO [46] MSFragger - (171-15) clear_mz_range_low = 0.0 2020-06-29 15:00:56,309 INFO [46] MSFragger - (171-15) clear_mz_range_high = 0.0 2020-06-29 15:00:56,325 INFO [46] MSFragger - (171-15) excluded_scan_list_file =
2020-06-29 15:00:56,343 INFO [46] MSFragger - (171-15) mass_diff_to_variable_mod = 0 2020-06-29 15:00:56,388 INFO [46] MSFragger - (171-15) variable_mod_01 = 15.994915 M 3 2020-06-29 15:00:56,404 INFO [46] MSFragger - (171-15) variable_mod_14 = 42.010565 [^ 3 2020-06-29 15:00:56,420 INFO [46] MSFragger - (171-15) add_C_cysteine = 57.021464 2020-06-29 15:00:56,437 INFO [46] MSFragger - (171-15) add_Cterm_peptide = 0.0 2020-06-29 15:00:56,454 INFO [46] MSFragger - (171-15) add_Cterm_protein = 0.0 2020-06-29 15:00:56,470 INFO [46] MSFragger - (171-15) add_Nterm_peptide = 0.0 2020-06-29 15:00:56,487 INFO [46] MSFragger - (171-15) add_Nterm_protein = 0.0 2020-06-29 15:00:56,769 INFO [46] MSFragger - (171-15) Number of unique peptides 2020-06-29 15:00:57,830 INFO [46] MSFragger - (171-15) of length 6: 212285 2020-06-29 15:00:57,852 INFO [46] MSFragger - (171-15) of length 7: 217633 2020-06-29 15:00:57,865 INFO [46] MSFragger - (171-15) of length 8: 201888 2020-06-29 15:00:57,878 INFO [46] MSFragger - (171-15) of length 9: 193753 2020-06-29 15:00:57,892 INFO [46] MSFragger - (171-15) of length 10: 177275 2020-06-29 15:00:57,892 INFO [46] MSFragger - (171-15) of length 11: 163085 2020-06-29 15:00:57,920 INFO [46] MSFragger - (171-15) of length 12: 150990 2020-06-29 15:00:57,933 INFO [46] MSFragger - (171-15) of length 13: 142741 2020-06-29 15:00:57,946 INFO [46] MSFragger - (171-15) of length 14: 128090 2020-06-29 15:00:57,959 INFO [46] MSFragger - (171-15) of length 15: 119912 2020-06-29 15:00:57,972 INFO [46] MSFragger - (171-15) of length 16: 109392 2020-06-29 15:00:57,987 INFO [46] MSFragger - (171-15) of length 17: 100142 2020-06-29 15:00:58,000 INFO [46] MSFragger - (171-15) of length 18: 93275 2020-06-29 15:00:58,017 INFO [46] MSFragger - (171-15) of length 19: 87569 2020-06-29 15:00:58,051 INFO [46] MSFragger - (171-15) of length 20: 79535 2020-06-29 15:00:58,067 INFO [46] MSFragger - (171-15) of length 21: 74378 2020-06-29 15:00:58,083 INFO [46] MSFragger - (171-15) of length 22: 68132 2020-06-29 15:00:58,099 INFO [46] MSFragger - (171-15) of length 23: 63255 2020-06-29 15:00:58,115 INFO [46] MSFragger - (171-15) of length 24: 59282 2020-06-29 15:00:58,130 INFO [46] MSFragger - (171-15) of length 25: 54941 2020-06-29 15:00:58,147 INFO [46] MSFragger - (171-15) of length 26: 50359 2020-06-29 15:00:58,164 INFO [46] MSFragger - (171-15) of length 27: 47784 2020-06-29 15:00:58,184 INFO [46] MSFragger - (171-15) of length 28: 44545 2020-06-29 15:00:58,200 INFO [46] MSFragger - (171-15) of length 29: 40944 2020-06-29 15:00:58,216 INFO [46] MSFragger - (171-15) of length 30: 38124 2020-06-29 15:00:58,232 INFO [46] MSFragger - (171-15) of length 31: 35163 2020-06-29 15:00:58,248 INFO [46] MSFragger - (171-15) of length 32: 32893 2020-06-29 15:00:58,264 INFO [46] MSFragger - (171-15) of length 33: 30232 2020-06-29 15:00:58,279 INFO [46] MSFragger - (171-15) of length 34: 27907 2020-06-29 15:00:58,302 INFO [46] MSFragger - (171-15) of length 35: 25405 2020-06-29 15:00:58,359 INFO [46] MSFragger - (171-15) of length 36: 24278 2020-06-29 15:00:58,432 INFO [46] MSFragger - (171-15) of length 37: 21517 2020-06-29 15:00:58,466 INFO [46] MSFragger - (171-15) of length 38: 20129 2020-06-29 15:00:58,514 INFO [46] MSFragger - (171-15) of length 39: 17931 2020-06-29 15:00:58,533 INFO [46] MSFragger - (171-15) of length 40: 17085 2020-06-29 15:00:58,549 INFO [46] MSFragger - (171-15) of length 41: 16075 2020-06-29 15:00:58,567 INFO [46] MSFragger - (171-15) of length 42: 14285 2020-06-29 15:00:58,583 INFO [46] MSFragger - (171-15) of length 43: 12514 2020-06-29 15:00:58,599 INFO [46] MSFragger - (171-15) of length 44: 10069 2020-06-29 15:00:58,616 INFO [46] MSFragger - (171-15) of length 45: 7890 2020-06-29 15:00:58,633 INFO [46] MSFragger - (171-15) of length 46: 5324 2020-06-29 15:00:58,651 INFO [46] MSFragger - (171-15) of length 47: 3472 2020-06-29 15:00:58,667 INFO [46] MSFragger - (171-15) of length 48: 2131 2020-06-29 15:00:58,683 INFO [46] MSFragger - (171-15) of length 49: 1118 2020-06-29 15:00:58,699 INFO [46] MSFragger - (171-15) of length 50: 702 2020-06-29 15:00:58,714 INFO [46] MSFragger - (171-15) In total 3045429 peptides. 2020-06-29 15:00:58,752 INFO [46] MSFragger - (171-15) Generated 4550203 modified peptides. 2020-06-29 15:00:58,768 INFO [46] MSFragger - (171-15) Number of peptides with more than 5000 modification patterns: 0 2020-06-29 15:01:00,421 INFO [46] MSFragger - (171-15) Selected fragment tolerance 0.25 Da. 2020-06-29 15:01:00,506 INFO [46] MSFragger - (171-15) 162270300 fragments to be searched in 1 slices (2.42 GB total) 2020-06-29 15:01:00,524 INFO [46] MSFragger - (171-15) Operating on slice 1 of 1:
2020-06-29 15:01:01,798 INFO [46] MSFragger - (171-15) Fragment index slice generated in 1.29 s 2020-06-29 15:01:21,271 INFO [46] MSFragger - (171-15) 001. 20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mgf 18.0 s | deisotoping 1.5 s 2020-06-29 15:01:30,870 INFO [46] MSFragger - (171-15) [progress: 293990/293990 (100%) - 40284 spectra/s] 7.3s | postprocessing 1.4 s 2020-06-29 15:01:31,531 INFO [46] MSFragger - (171-15) *FIRST SEARCH DONE IN 0.815 MIN** 2020-06-29 15:01:31,550 INFO [46] MSFragger - (171-15) ***MASS CALIBRATION** 2020-06-29 15:01:31,566 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:31,582 INFO [46] MSFragger - (171-15) | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
2020-06-29 15:01:31,597 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:31,614 INFO [46] MSFragger - (171-15) Run | Median MAD | Median MAD | Median MAD | Median MAD
2020-06-29 15:01:48,876 INFO [46] MSFragger - (171-15) 001 | 2.07 4.01 | 0.13 3.31 | -2.02 6.34 | -1.36 6.38
2020-06-29 15:01:48,899 INFO [46] MSFragger - (171-15) -----|---------------|---------------|---------------|--------------- 2020-06-29 15:01:48,914 INFO [46] MSFragger - (171-15) Finding the optimal parameters: 2020-06-29 15:01:48,929 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:01:48,947 INFO [46] MSFragger - (171-15) MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50
2020-06-29 15:01:48,963 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,371 INFO [46] MSFragger - (171-15) Count | 117029| 126087| 131713| 134096| 133026| skip rest 2020-06-29 15:02:53,395 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,414 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:02:53,432 INFO [46] MSFragger - (171-15) Peaks | 500_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1
2020-06-29 15:02:53,451 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:03:44,335 INFO [46] MSFragger - (171-15) Count | 135126| 135126| 135126| 134096| skip rest 2020-06-29 15:03:44,360 INFO [46] MSFragger - (171-15) -------|-------|-------|-------|-------|-------|------- 2020-06-29 15:03:44,378 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:44,395 INFO [46] MSFragger - (171-15) Int. | 1
2020-06-29 15:03:44,423 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,343 INFO [46] MSFragger - (171-15) Count | 136626 2020-06-29 15:03:57,369 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,387 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:03:57,405 INFO [46] MSFragger - (171-15) Rm P. | 1
2020-06-29 15:03:57,424 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:04:10,193 INFO [46] MSFragger - (171-15) Count | 136666 2020-06-29 15:04:10,213 INFO [46] MSFragger - (171-15) -------|------- 2020-06-29 15:04:10,232 INFO [46] MSFragger - (171-15) New fragment_mass_tolerance = 15 PPM 2020-06-29 15:04:10,250 INFO [46] MSFragger - (171-15) New use_topN_peaks = 175 2020-06-29 15:04:10,269 INFO [46] MSFragger - (171-15) New minimum_ratio = 0.000000 2020-06-29 15:04:10,288 INFO [46] MSFragger - (171-15) New intensity_transform = 1 2020-06-29 15:04:10,310 INFO [46] MSFragger - (171-15) New remove_precursor_peak = 1 2020-06-29 15:04:10,328 INFO [46] MSFragger - (171-15) **MASS CALIBRATION DONE IN 2.644 MIN* 2020-06-29 15:04:10,347 INFO [46] MSFragger - (171-15) ****MAIN SEARCH**** 2020-06-29 15:04:10,366 INFO [46] MSFragger - (171-15) Checking database... 2020-06-29 15:04:10,383 INFO [46] MSFragger - (171-15) Parameters: 2020-06-29 15:04:10,401 INFO [46] MSFragger - (171-15) num_threads = 40 2020-06-29 15:04:10,418 INFO [46] MSFragger - (171-15) database_name = D:\200ng_K562\PD_4786_Fragger\temp171\Human_2020-05-05-R-C-UP000005640_combined.fasta 2020-06-29 15:04:10,437 INFO [46] MSFragger - (171-15) decoyprefix = rev 2020-06-29 15:04:10,454 INFO [46] MSFragger - (171-15) precursor_mass_lower = -50.0 2020-06-29 15:04:10,471 INFO [46] MSFragger - (171-15) precursor_mass_upper = 50.0 2020-06-29 15:04:10,488 INFO [46] MSFragger - (171-15) precursor_mass_units = 1 2020-06-29 15:04:10,504 INFO [46] MSFragger - (171-15) precursor_true_tolerance = 20.0 2020-06-29 15:04:10,521 INFO [46] MSFragger - (171-15) precursor_true_units = 1 2020-06-29 15:04:10,538 INFO [46] MSFragger - (171-15) fragment_mass_tolerance = 15.0 2020-06-29 15:04:10,558 INFO [46] MSFragger - (171-15) fragment_mass_units = 1 2020-06-29 15:04:10,575 INFO [46] MSFragger - (171-15) calibrate_mass = 2 2020-06-29 15:04:10,592 INFO [46] MSFragger - (171-15) write_calibrated_mgf = false 2020-06-29 15:04:10,617 INFO [46] MSFragger - (171-15) isotope_error = 0/1/2 2020-06-29 15:04:10,644 INFO [46] MSFragger - (171-15) mass_offsets = 0 2020-06-29 15:04:10,668 INFO [46] MSFragger - (171-15) labile_search_mode = OFF 2020-06-29 15:04:10,688 INFO [46] MSFragger - (171-15) precursor_mass_mode = SELECTED 2020-06-29 15:04:10,705 INFO [46] MSFragger - (171-15) localize_delta_mass = false 2020-06-29 15:04:10,740 INFO [46] MSFragger - (171-15) delta_mass_exclude_ranges = (-1.5,3.5) 2020-06-29 15:04:10,753 INFO [46] MSFragger - (171-15) fragment_ion_series = b,y 2020-06-29 15:04:10,776 INFO [46] MSFragger - (171-15) diagnostic_intensity_filter = 0.0 2020-06-29 15:04:10,794 INFO [46] MSFragger - (171-15) Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 2020-06-29 15:04:10,811 INFO [46] MSFragger - (171-15) diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 2020-06-29 15:04:10,827 INFO [46] MSFragger - (171-15) search_enzyme_name = Trypsin 2020-06-29 15:04:10,840 INFO [46] MSFragger - (171-15) search_enzyme_cutafter = KR 2020-06-29 15:04:10,861 INFO [46] MSFragger - (171-15) search_enzyme_butnotafter = P 2020-06-29 15:04:10,878 INFO [46] MSFragger - (171-15) num_enzyme_termini = 2 2020-06-29 15:04:10,895 INFO [46] MSFragger - (171-15) allowed_missed_cleavage = 2 2020-06-29 15:04:10,916 INFO [46] MSFragger - (171-15) clip_nTerm_M = true 2020-06-29 15:04:10,950 INFO [46] MSFragger - (171-15) allow_multiple_variable_mods_on_residue = true 2020-06-29 15:04:10,967 INFO [46] MSFragger - (171-15) max_variable_mods_per_peptide = 3 2020-06-29 15:04:10,986 INFO [46] MSFragger - (171-15) max_variable_mods_combinations = 5000 2020-06-29 15:04:11,005 INFO [46] MSFragger - (171-15) output_file_extension = pepXML 2020-06-29 15:04:11,023 INFO [46] MSFragger - (171-15) output_format = pepXML 2020-06-29 15:04:11,043 INFO [46] MSFragger - (171-15) output_report_topN = 1 2020-06-29 15:04:11,061 INFO [46] MSFragger - (171-15) output_max_expect = 50.0 2020-06-29 15:04:11,079 INFO [46] MSFragger - (171-15) report_alternative_proteins = true 2020-06-29 15:04:11,097 INFO [46] MSFragger - (171-15) override_charge = false 2020-06-29 15:04:11,114 INFO [46] MSFragger - (171-15) precursor_charge_low = 1 2020-06-29 15:04:11,132 INFO [46] MSFragger - (171-15) precursor_charge_high = 4 2020-06-29 15:04:11,150 INFO [46] MSFragger - (171-15) digest_min_length = 6 2020-06-29 15:04:11,170 INFO [46] MSFragger - (171-15) digest_max_length = 50 2020-06-29 15:04:11,188 INFO [46] MSFragger - (171-15) digest_mass_range_low = 500.0 2020-06-29 15:04:11,206 INFO [46] MSFragger - (171-15) digest_mass_range_high = 5000.0 2020-06-29 15:04:11,224 INFO [46] MSFragger - (171-15) max_fragment_charge = 2 2020-06-29 15:04:11,241 INFO [46] MSFragger - (171-15) deisotope = 1 2020-06-29 15:04:11,259 INFO [46] MSFragger - (171-15) track_zero_topN = 0 2020-06-29 15:04:11,280 INFO [46] MSFragger - (171-15) zero_bin_accept_expect = 0.0 2020-06-29 15:04:11,298 INFO [46] MSFragger - (171-15) zero_bin_mult_expect = 1.0 2020-06-29 15:04:11,316 INFO [46] MSFragger - (171-15) add_topN_complementary = 0 2020-06-29 15:04:11,334 INFO [46] MSFragger - (171-15) minimum_peaks = 15 2020-06-29 15:04:11,351 INFO [46] MSFragger - (171-15) use_topN_peaks = 175 2020-06-29 15:04:11,369 INFO [46] MSFragger - (171-15) minIonsScoring = 2 2020-06-29 15:04:11,386 INFO [46] MSFragger - (171-15) min_matched_fragments = 3 2020-06-29 15:04:11,406 INFO [46] MSFragger - (171-15) minimum_ratio = 0.0 2020-06-29 15:04:11,424 INFO [46] MSFragger - (171-15) intensity_transform = 1 2020-06-29 15:04:11,443 INFO [46] MSFragger - (171-15) remove_precursor_peak = 1 2020-06-29 15:04:11,461 INFO [46] MSFragger - (171-15) remove_precursor_range = -1.5,1.5 2020-06-29 15:04:11,480 INFO [46] MSFragger - (171-15) clear_mz_range_low = 0.0 2020-06-29 15:04:11,499 INFO [46] MSFragger - (171-15) clear_mz_range_high = 0.0 2020-06-29 15:04:11,517 INFO [46] MSFragger - (171-15) excluded_scan_list_file =
2020-06-29 15:04:11,537 INFO [46] MSFragger - (171-15) mass_diff_to_variable_mod = 0 2020-06-29 15:04:11,554 INFO [46] MSFragger - (171-15) variable_mod_01 = 15.994915 M 3 2020-06-29 15:04:11,572 INFO [46] MSFragger - (171-15) variable_mod_02 = 0.984016 NQ 3 2020-06-29 15:04:11,591 INFO [46] MSFragger - (171-15) variable_mod_14 = 42.010565 [^ 3 2020-06-29 15:04:11,609 INFO [46] MSFragger - (171-15) add_C_cysteine = 57.021464 2020-06-29 15:04:11,626 INFO [46] MSFragger - (171-15) add_Cterm_peptide = 0.0 2020-06-29 15:04:11,646 INFO [46] MSFragger - (171-15) add_Cterm_protein = 0.0 2020-06-29 15:04:11,663 INFO [46] MSFragger - (171-15) add_Nterm_peptide = 0.0 2020-06-29 15:04:11,682 INFO [46] MSFragger - (171-15) add_Nterm_protein = 0.0 2020-06-29 15:04:11,700 INFO [46] MSFragger - (171-15) Number of unique peptides 2020-06-29 15:04:12,278 INFO [46] MSFragger - (171-15) of length 6: 244659 2020-06-29 15:04:12,297 INFO [46] MSFragger - (171-15) of length 7: 262418 2020-06-29 15:04:12,314 INFO [46] MSFragger - (171-15) of length 8: 253525 2020-06-29 15:04:12,332 INFO [46] MSFragger - (171-15) of length 9: 251178 2020-06-29 15:04:12,349 INFO [46] MSFragger - (171-15) of length 10: 238922 2020-06-29 15:04:12,366 INFO [46] MSFragger - (171-15) of length 11: 227508 2020-06-29 15:04:12,385 INFO [46] MSFragger - (171-15) of length 12: 217702 2020-06-29 15:04:12,402 INFO [46] MSFragger - (171-15) of length 13: 213375 2020-06-29 15:04:12,420 INFO [46] MSFragger - (171-15) of length 14: 198654 2020-06-29 15:04:12,437 INFO [46] MSFragger - (171-15) of length 15: 190687 2020-06-29 15:04:12,454 INFO [46] MSFragger - (171-15) of length 16: 178542 2020-06-29 15:04:12,471 INFO [46] MSFragger - (171-15) of length 17: 168048 2020-06-29 15:04:12,488 INFO [46] MSFragger - (171-15) of length 18: 162390 2020-06-29 15:04:12,507 INFO [46] MSFragger - (171-15) of length 19: 157944 2020-06-29 15:04:12,525 INFO [46] MSFragger - (171-15) of length 20: 144011 2020-06-29 15:04:12,543 INFO [46] MSFragger - (171-15) of length 21: 137909 2020-06-29 15:04:12,560 INFO [46] MSFragger - (171-15) of length 22: 129721 2020-06-29 15:04:12,577 INFO [46] MSFragger - (171-15) of length 23: 121623 2020-06-29 15:04:12,594 INFO [46] MSFragger - (171-15) of length 24: 116623 2020-06-29 15:04:12,611 INFO [46] MSFragger - (171-15) of length 25: 109515 2020-06-29 15:04:12,629 INFO [46] MSFragger - (171-15) of length 26: 102416 2020-06-29 15:04:12,646 INFO [46] MSFragger - (171-15) of length 27: 97732 2020-06-29 15:04:12,663 INFO [46] MSFragger - (171-15) of length 28: 95936 2020-06-29 15:04:12,680 INFO [46] MSFragger - (171-15) of length 29: 85854 2020-06-29 15:04:12,697 INFO [46] MSFragger - (171-15) of length 30: 81437 2020-06-29 15:04:12,713 INFO [46] MSFragger - (171-15) of length 31: 77251 2020-06-29 15:04:12,731 INFO [46] MSFragger - (171-15) of length 32: 73282 2020-06-29 15:04:12,750 INFO [46] MSFragger - (171-15) of length 33: 68739 2020-06-29 15:04:12,768 INFO [46] MSFragger - (171-15) of length 34: 64540 2020-06-29 15:04:12,786 INFO [46] MSFragger - (171-15) of length 35: 58977 2020-06-29 15:04:12,803 INFO [46] MSFragger - (171-15) of length 36: 57757 2020-06-29 15:04:12,821 INFO [46] MSFragger - (171-15) of length 37: 53103 2020-06-29 15:04:12,838 INFO [46] MSFragger - (171-15) of length 38: 49710 2020-06-29 15:04:12,855 INFO [46] MSFragger - (171-15) of length 39: 45022 2020-06-29 15:04:12,875 INFO [46] MSFragger - (171-15) of length 40: 43118 2020-06-29 15:04:12,892 INFO [46] MSFragger - (171-15) of length 41: 40552 2020-06-29 15:04:12,908 INFO [46] MSFragger - (171-15) of length 42: 36967 2020-06-29 15:04:12,925 INFO [46] MSFragger - (171-15) of length 43: 31840 2020-06-29 15:04:12,942 INFO [46] MSFragger - (171-15) of length 44: 25446 2020-06-29 15:04:12,958 INFO [46] MSFragger - (171-15) of length 45: 19263 2020-06-29 15:04:12,975 INFO [46] MSFragger - (171-15) of length 46: 12575 2020-06-29 15:04:12,994 INFO [46] MSFragger - (171-15) of length 47: 7828 2020-06-29 15:04:13,011 INFO [46] MSFragger - (171-15) of length 48: 4572 2020-06-29 15:04:13,028 INFO [46] MSFragger - (171-15) of length 49: 2342 2020-06-29 15:04:13,046 INFO [46] MSFragger - (171-15) of length 50: 1366 2020-06-29 15:04:13,086 INFO [46] MSFragger - (171-15) In total 4962579 peptides. 2020-06-29 15:04:14,589 INFO [46] MSFragger - (171-15) Generated 42341316 modified peptides. 2020-06-29 15:04:14,607 INFO [46] MSFragger - (171-15) Number of peptides with more than 5000 modification patterns: 0 2020-06-29 15:04:19,430 INFO [46] MSFragger - (171-15) Selected fragment tolerance 0.08 Da. 2020-06-29 15:04:20,300 INFO [46] MSFragger - (171-15) 2267595348 fragments to be searched in 1 slices (33.79 GB total) 2020-06-29 15:04:20,322 INFO [46] MSFragger - (171-15) Operating on slice 1 of 1:
2020-06-29 15:04:42,729 INFO [46] MSFragger - (171-15) Fragment index slice generated in 22.43 s 2020-06-29 15:04:49,108 INFO [46] MSFragger - (171-15) 001. 20191021_K562_200ng_90min_Slot1-1_01_4786_53113.mzBIN_calibrated 6.4 s 2020-06-29 15:05:07,440 INFO [46] MSFragger - (171-15) [progress: 87913/292598 (30%) - 8440 spectra/s] 2020-06-29 15:05:30,307 INFO [46] MSFragger - (171-15) [progress: 292598/292598 (100%) - 15961 spectra/s] 18.3s | postprocessing 22.3 s 2020-06-29 15:05:30,850 INFO [46] MSFragger - (171-15) MAIN SEARCH DONE IN 1.344 MIN 2020-06-29 15:05:30,871 INFO [46] MSFragger - (171-15) ***TOTAL TIME 4.803 MIN**** 2020-06-29 15:05:38,821 INFO [46] MSFragger - (171-15) MSFragger Running Time --0:4:59 2020-06-29 15:05:38,846 ERROR [46] MSFragger - (171-15) Error: An item with the same key has already been added. 2020-06-29 15:05:38,899 ERROR [46] MSFragger - (171-15) Could not process spectra due to following exception: An item with the same key has already been added. 2020-06-29 15:05:38,966 ERROR [46] JobManager+b - Exception caught -> Processing of Job (ID: 171) fails. System.ArgumentException: An item with the same key has already been added. at System.ThrowHelper.ThrowArgumentException(ExceptionResource resource) at System.Collections.Generic.Dictionary
2.Insert(TKey key, TValue value, Boolean add) at MSFraggerPDv24.MSFragger.OnSpectraSentForSearch(IProcessingNode sender, MassSpectrumCollection spectraSent) at Thermo.Magellan.BL.Processing.PeptideAndProteinIdentificationNode.OnResultsSent(IProcessingNode sender, MassSpectrumCollection spectra) at Thermo.Magellan.BL.Processing.ProcessingNodeBase3.SendResults(TResult1 result) at Thermo.Magellan.RetrieverNodes.SpectrumSelectorNode.h() at Thermo.Magellan.RetrieverNodes.SpectrumSelectorNode.OnAllParentNodesFinished() at Thermo.Magellan.BL.Processing.ProcessingNodeBase.FireProcessingFinishedEvent(ResultsArguments eventArgs) at Thermo.Magellan.RetrieverNodes.SpectrumFilesNode.Process() at Thermo.Magellan.BL.Jobs.ProcessingJob.ExecuteNodesIncludingPostProcessingNodes(Action doExecuteNodes, Stopwatch timer) at Thermo.Magellan.BL.Jobs.CompositeJob.ExecuteChildJobs() at Thermo.Magellan.Services.JobManager.b.b() 2020-06-29 15:05:38,983 INFO [46] DataAccessBase - Removing Scratch file: D:\200ng_K562\PD_4786_Fragger\20191021_K562_200ng_90min_Slot1-1_01_4786_53113-(3).msf.scratch. 2020-06-29 15:05:39,013 DEBUG [46] ReportFile - Closing file [171]: D:\200ng_K562\PD_4786_Fragger\20191021_K562_200ng_90min_Slot1-1_01_4786_53113-(3).msf 2020-06-29 15:05:39,024 DEBUG [46] JobManager - JobQueue (2 jobs queued)