Starting DIA-Umpire conversion [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1509/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 8267/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 13215/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 16403/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 19407/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 22534/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 25651/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 28574/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 31438/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 34244/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 37034/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 39862/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 42533/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 45404/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 48189/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 50869/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 53618/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 56356/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 59165/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 62087/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 65105/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 68441/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 72277/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 76862/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 82495/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 88850/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 94952/98373 [0001-231030-A1-LT2 (1 of 6)] [step 1 of 7] assigning spectra to DIA windows: 98373/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 2520/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 8073/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 12423/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 14963/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 17582/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 20140/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 22643/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 25173/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 27649/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 30065/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 32429/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 34801/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 37172/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 39528/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 41946/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 44421/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 46856/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 49191/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 51452/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 53759/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 56087/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 58405/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 60877/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 63397/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 66063/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 68885/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 72009/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 75804/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 80403/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 85446/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 90845/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 95711/98373 [0001-231030-A1-LT2 (1 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 98373/98373 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 1/1929 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 133/1929 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 598/1929 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 1268/1929 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 1673/1929 [0001-231030-A1-LT2 (1 of 6)] [step 3 of 7] building peak curves: 1929/1929 [0001-231030-A1-LT2 (1 of 6)] [step 4 of 7] smoothing peak curves: 813830/813830 [0001-231030-A1-LT2 (1 of 6)] [step 5 of 7] clustering peak curves: 1/815677 [0001-231030-A1-LT2 (1 of 6)] [step 5 of 7] clustering peak curves: 333200/815677 [0001-231030-A1-LT2 (1 of 6)] [step 5 of 7] clustering peak curves: 815677/815677 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 2/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 2429/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 7085/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 11964/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 14486/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 17096/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 19606/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 21939/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 24278/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 26581/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 28899/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 31143/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 33388/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 35669/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 37934/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 40184/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 42387/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 44669/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 46949/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 49116/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 51280/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 53450/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 55717/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 58035/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 60375/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 62859/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 65386/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 68187/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 71111/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 74701/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 78994/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 81910/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 86655/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 92251/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 97102/98373 [0001-231030-A1-LT2 (1 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 98373/98373 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 1/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 2/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 4/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 5/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 6/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 7/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 8/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 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processing DIA window: 23/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 26/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 27/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 28/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 29/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 30/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 31/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 32/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 33/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 34/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 35/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 36/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 37/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 38/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 39/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 40/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 41/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 42/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 44/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 45/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 46/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 47/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 48/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 49/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 50/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 51/52 [0001-231030-A1-LT2 (1 of 6)] [step 7 of 7] processing DIA window: 52/52 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 1/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 4/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 201/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 2311/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 5387/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 8370/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 11340/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 14529/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 17664/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 20765/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 23905/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 27029/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 29992/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 33149/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 36462/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 39741/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 43079/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 46967/47258 [0001-231030-A1-LT2 (1 of 6)] writing spectra: 47258/47258 [0001-231030-A1-LT2 (1 of 6)] writing chromatograms: 1/3 [0001-231030-A1-LT2 (1 of 6)] writing chromatograms: 3/3 [0001-231030-A1-LT2 (1 of 6)] writing indexes: 1/0 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 5713/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 11826/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 16598/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 21272/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 25724/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 29919/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 34137/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 38310/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 42541/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 45905/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 50055/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 53481/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 57961/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 62140/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 65668/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 70846/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 75675/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 82602/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 87407/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 91731/95677 [0002-231030-A1-THY (2 of 6)] [step 1 of 7] assigning spectra to DIA windows: 95677/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 36/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 4959/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 8838/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 12778/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 16313/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 19229/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 22454/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 25189/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 27726/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 30826/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 34291/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 37732/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 41136/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 44307/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 47336/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 49129/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 50098/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 53506/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 57499/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 62334/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 68014/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 73512/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 79780/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 85951/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 90302/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 93836/95677 [0002-231030-A1-THY (2 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 95677/95677 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 47/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 280/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 507/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 734/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 919/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1027/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1090/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1179/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1246/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1343/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1438/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1578/1877 [0002-231030-A1-THY (2 of 6)] [step 3 of 7] building peak curves: 1877/1877 [0002-231030-A1-THY (2 of 6)] [step 4 of 7] smoothing peak curves: 520358/520358 [0002-231030-A1-THY (2 of 6)] [step 5 of 7] clustering peak curves: 1/521518 [0002-231030-A1-THY (2 of 6)] [step 5 of 7] clustering peak curves: 521518/521518 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 5475/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 11024/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 15123/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 19055/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 22758/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 26594/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 30278/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 33702/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 37088/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 40855/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 44627/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 48306/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 52477/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 56906/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 61970/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 67695/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 73879/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 80593/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 87383/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 93562/95677 [0002-231030-A1-THY (2 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 95677/95677 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 1/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 4/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 7/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 9/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 10/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 11/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 14/52 [0002-231030-A1-THY (2 of 6)] [step 7 of 7] processing DIA window: 15/52 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[0002-231030-A1-THY (2 of 6)] writing spectra: 5558/22442 [0002-231030-A1-THY (2 of 6)] writing spectra: 9029/22442 [0002-231030-A1-THY (2 of 6)] writing spectra: 12474/22442 [0002-231030-A1-THY (2 of 6)] writing spectra: 15848/22442 [0002-231030-A1-THY (2 of 6)] writing spectra: 19346/22442 [0002-231030-A1-THY (2 of 6)] writing spectra: 22442/22442 [0002-231030-A1-THY (2 of 6)] writing chromatograms: 1/3 [0002-231030-A1-THY (2 of 6)] writing chromatograms: 3/3 [0002-231030-A1-THY (2 of 6)] writing indexes: 1/0 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 2202/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 8664/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 13494/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 16825/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 19964/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 23294/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 26531/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 29664/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 32742/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 35817/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 38815/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 41970/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 44958/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 47924/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 51072/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 54290/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 57821/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 61591/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 66136/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 71169/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 76817/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 83304/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 90146/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 96253/97231 [0003-231030-B1-THY (3 of 6)] [step 1 of 7] assigning spectra to DIA windows: 97231/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] 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6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 37408/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 40128/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 42861/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 45691/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 48557/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 51422/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 54442/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 57729/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 61108/97231 [0003-231030-B1-THY (3 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 65114/97231 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(3 of 6)] [step 7 of 7] processing DIA window: 10/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 11/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 12/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 13/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 15/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 17/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 18/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 19/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 20/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 21/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 22/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 24/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 25/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 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processing DIA window: 46/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 47/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 48/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 49/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 50/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 51/52 [0003-231030-B1-THY (3 of 6)] [step 7 of 7] processing DIA window: 52/52 [0003-231030-B1-THY (3 of 6)] writing spectra: 1/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 179/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 2976/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 6501/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 10176/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 13718/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 17304/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 20876/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 24426/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 28397/30276 [0003-231030-B1-THY (3 of 6)] writing spectra: 30276/30276 [0003-231030-B1-THY (3 of 6)] writing chromatograms: 1/3 [0003-231030-B1-THY (3 of 6)] writing chromatograms: 3/3 [0003-231030-B1-THY (3 of 6)] writing indexes: 1/0 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 3795/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 11408/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 14844/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 17885/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 20784/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 23606/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 26422/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 29184/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 31888/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 34559/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 37147/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 39705/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 42231/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 44767/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 47298/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 49838/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 52234/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 54612/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 56808/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 58966/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 61135/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 63458/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 65856/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 68240/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 70672/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 73133/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 75733/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 78526/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 81418/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 84592/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 87838/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 91335/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 94765/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 98405/98796 [0012-23125-A1-SAA (4 of 6)] [step 1 of 7] assigning spectra to DIA windows: 98796/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 5469/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 11929/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 15516/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 18762/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 21772/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 24730/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 27393/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 29941/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 32346/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 34839/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 37252/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 39661/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 42121/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 44584/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 47045/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 49505/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 51920/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 54219/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 56205/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 58265/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 60290/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 62623/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 65020/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 67493/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 69967/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 72554/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 75289/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 78163/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 81403/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 84934/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 88755/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 92633/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 96826/98796 [0012-23125-A1-SAA (4 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 98796/98796 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 1/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 362/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 557/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 769/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 972/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 1195/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 1446/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 1697/1938 [0012-23125-A1-SAA (4 of 6)] [step 3 of 7] building peak curves: 1938/1938 [0012-23125-A1-SAA (4 of 6)] [step 4 of 7] smoothing peak curves: 692273/692273 [0012-23125-A1-SAA (4 of 6)] [step 5 of 7] clustering peak curves: 1/693171 [0012-23125-A1-SAA (4 of 6)] [step 5 of 7] clustering peak curves: 693171/693171 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 2/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 4970/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 11268/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 15049/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 18311/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 21281/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 24263/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 27141/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 29925/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 32728/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 35365/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 37859/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 40437/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 42998/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 45499/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 48033/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 50493/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 52886/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 55226/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 57578/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 60003/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 62415/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 64876/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 67436/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 70051/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 72795/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 75722/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 78846/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 82210/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 86007/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 90216/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 94200/98796 [0012-23125-A1-SAA (4 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 98796/98796 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 1/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 2/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 3/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 5/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 8/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 9/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 10/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 11/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 12/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 13/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 14/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 17/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 18/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 19/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 20/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 21/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 22/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 23/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 24/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 27/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 28/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 29/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 30/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 31/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 32/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 33/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 34/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 35/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 36/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 37/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 38/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 39/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 40/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 41/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 42/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 43/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 45/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 46/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 47/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 48/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 49/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 50/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 51/52 [0012-23125-A1-SAA (4 of 6)] [step 7 of 7] processing DIA window: 52/52 [0012-23125-A1-SAA (4 of 6)] writing spectra: 1/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 21/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 445/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 3500/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 6599/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 9774/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 12975/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 16278/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 19385/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 22480/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 25599/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 28748/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 31932/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 35208/38386 [0012-23125-A1-SAA (4 of 6)] writing spectra: 38386/38386 [0012-23125-A1-SAA (4 of 6)] writing chromatograms: 1/3 [0012-23125-A1-SAA (4 of 6)] writing chromatograms: 3/3 [0012-23125-A1-SAA (4 of 6)] writing indexes: 1/0 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 1998/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 8980/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 14388/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 18156/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 21653/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 25032/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 28328/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 31709/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 34974/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 38228/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 41275/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 44471/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 47676/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 50862/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 53860/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 56860/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 59887/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 63058/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 66336/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 69868/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 73681/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 77863/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 82744/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 88280/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 93722/98341 [0014-23125-B1-ALL (5 of 6)] [step 1 of 7] assigning spectra to DIA windows: 98341/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 1163/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 7983/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 13493/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 17100/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 20298/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 23398/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 26313/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 29199/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 32049/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 34850/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 37537/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 40123/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 42737/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 45403/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 48142/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 50696/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 53267/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 55812/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 58367/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 61056/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 63772/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 66746/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 69973/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 73398/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 77149/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 81286/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 85738/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 90491/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 94940/98341 [0014-23125-B1-ALL (5 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 98341/98341 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 1/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 97/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 503/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 727/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 939/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 1195/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 1476/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 1837/1929 [0014-23125-B1-ALL (5 of 6)] [step 3 of 7] building peak curves: 1929/1929 [0014-23125-B1-ALL (5 of 6)] [step 4 of 7] smoothing peak curves: 672640/672640 [0014-23125-B1-ALL (5 of 6)] [step 5 of 7] clustering peak curves: 1/673245 [0014-23125-B1-ALL (5 of 6)] [step 5 of 7] clustering peak curves: 105452/673245 [0014-23125-B1-ALL (5 of 6)] [step 5 of 7] clustering peak curves: 673245/673245 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 2/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 5208/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 11659/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 15402/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 18875/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 21881/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 24960/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 27765/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 30636/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 33413/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 35930/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 38393/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 40947/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 43637/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 46394/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 49133/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 51842/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 54530/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 57225/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 59873/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 62630/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 65562/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 68435/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 71772/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 75280/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 79465/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 84160/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 89187/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 94362/98341 [0014-23125-B1-ALL (5 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 98341/98341 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 1/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 2/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 3/52 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window: 39/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 40/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 41/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 42/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 44/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 46/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 47/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 48/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 49/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 50/52 [0014-23125-B1-ALL (5 of 6)] [step 7 of 7] processing DIA window: 52/52 [0014-23125-B1-ALL (5 of 6)] writing spectra: 1/32429 [0014-23125-B1-ALL (5 of 6)] writing spectra: 4/32429 [0014-23125-B1-ALL (5 of 6)] writing spectra: 706/32429 [0014-23125-B1-ALL (5 of 6)] writing spectra: 4164/32429 [0014-23125-B1-ALL (5 of 6)] writing spectra: 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of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 60410/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 62676/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 64935/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 67226/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 69563/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 71905/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 74346/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 76889/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 79578/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 82367/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 85398/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 88710/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 92341/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 95893/100012 [0016-23125-A1-ALL (6 of 6)] [step 2 of 7] reading MS1/MS2 spectra into scan collection: 100012/100012 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 1/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 482/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 689/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 894/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 1160/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 1574/1962 [0016-23125-A1-ALL (6 of 6)] [step 3 of 7] building peak curves: 1962/1962 [0016-23125-A1-ALL (6 of 6)] [step 4 of 7] smoothing peak curves: 791455/791455 [0016-23125-A1-ALL (6 of 6)] [step 5 of 7] clustering peak curves: 1/792126 [0016-23125-A1-ALL (6 of 6)] [step 5 of 7] clustering peak curves: 713228/792126 [0016-23125-A1-ALL (6 of 6)] [step 5 of 7] clustering peak curves: 792126/792126 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 3500/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 9636/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 13696/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 16654/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 19424/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 22055/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 24633/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 27124/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 29538/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 31984/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 34376/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 36717/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 39024/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 41225/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 43498/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 45738/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 48004/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 50175/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 52297/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 54399/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 56478/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 58618/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 60759/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 62945/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 65161/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 67406/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 69695/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 72011/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 74395/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 76862/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 79464/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 82170/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 85000/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 88099/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 91507/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 94798/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 98800/100012 [0016-23125-A1-ALL (6 of 6)] [step 6 of 7] reading MS2 spectra into scan collection: 100012/100012 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 1/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 2/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 3/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 4/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 5/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 7/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 8/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 9/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 10/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 11/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 12/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 13/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 14/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 15/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 16/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 18/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 19/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 20/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 21/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 22/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 23/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 24/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 25/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 26/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 27/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 28/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 29/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 30/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 31/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 32/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 33/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 34/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 35/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 36/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 38/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 39/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 40/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 41/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 43/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 45/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 46/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 47/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 48/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 49/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 50/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 51/52 [0016-23125-A1-ALL (6 of 6)] [step 7 of 7] processing DIA window: 52/52 [0016-23125-A1-ALL (6 of 6)] writing spectra: 1/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 4/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 100/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 1537/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 3446/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 5779/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 7731/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 9974/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 13307/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 16655/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 19939/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 22175/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 25394/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 28008/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 30862/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 33828/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 37108/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 40194/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 43512/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 46927/48960 [0016-23125-A1-ALL (6 of 6)] writing spectra: 48960/48960 [0016-23125-A1-ALL (6 of 6)] writing chromatograms: 1/3 [0016-23125-A1-ALL (6 of 6)] writing chromatograms: 3/3 [0016-23125-A1-ALL (6 of 6)] writing indexes: 1/0 Starting search... Detecting decoy prefix in amyloid-simple.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_amyloid-simple.fasta. MSFragger version MSFragger-3.8 Batmass-IO version 1.28.12 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 17.0.1, OpenJDK 64-Bit Server VM, Oracle Corporation JVM started with 15 GB memory Checking database... Parameter 'min_sequence_matches' was not supplied. Using default value: 2 Parameter 'write_mzbin_all' was not supplied. Using default value: 0 Parameter 'group_variable' was not supplied. Using default value: 0 Parameter 'require_precursor' was not supplied. Using default value: 0 Parameter 'reuse_dia_fragment_peaks' was not supplied. Using default value: 0 Parameter 'activation_types' was not supplied. Using default value: all Checking spectral files... F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0002-231030-A1-THY-diaumpire.mzML: Scans = 22442 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0003-231030-B1-THY-diaumpire.mzML: Scans = 30276 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0014-23125-B1-ALL-diaumpire.mzML: Scans = 32429 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0016-23125-A1-ALL-diaumpire.mzML: Scans = 48960 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0012-23125-A1-SAA-diaumpire.mzML: Scans = 38384 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0001-231030-A1-LT2-diaumpire.mzML: Scans = 47257 ************************************MAIN SEARCH************************************ Checking database... Parameter 'min_sequence_matches' was not supplied. Using default value: 2 Parameter 'write_mzbin_all' was not supplied. Using default value: 0 Parameter 'group_variable' was not supplied. Using default value: 0 Parameter 'require_precursor' was not supplied. Using default value: 0 Parameter 'reuse_dia_fragment_peaks' was not supplied. Using default value: 0 Parameter 'activation_types' was not supplied. Using default value: all Parameter 'remainder_fragment_masses' was not supplied. Using default value: Parameters: num_threads = 16 database_name = F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\decoy_amyloid-simple.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 = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 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 = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = Trypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = P allowed_missed_cleavage_1 = 0 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 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 = 1 override_charge = 0 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 = 1 deisotope = 1 deneutralloss = 1 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 activation_types = all group_variable = 0 require_precursor = 0 reuse_dia_fragment_peaks = 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 = 1 add_C_cysteine = 57.021464 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 5: 286 of length 6: 256 of length 7: 233 of length 8: 192 of length 9: 224 of length 10: 130 of length 11: 192 of length 12: 113 of length 13: 114 of length 14: 105 of length 15: 182 of length 16: 85 of length 17: 95 of length 18: 71 of length 19: 119 of length 20: 81 of length 21: 60 of length 22: 82 of length 23: 76 of length 24: 45 of length 25: 54 of length 26: 35 of length 27: 23 of length 28: 17 of length 29: 25 of length 30: 37 of length 31: 13 of length 32: 28 of length 33: 23 of length 34: 31 of length 35: 46 of length 36: 17 of length 37: 54 of length 38: 31 of length 39: 13 of length 40: 7 of length 41: 5 of length 42: 19 of length 43: 7 of length 44: 12 of length 45: 5 of length 46: 1 of length 47: 2 of length 56: 1 In total 3247 peptides. Generated 3247 modified peptides. Number of peptides with more than 5500 modification patterns: 0 Selected fragment index width 0.10 Da. 92240 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. 0001-231030-A1-LT2-diaumpire.mzML 2.3 s | deisotoping 0.5 s [progress: 47238/47238 (100%) - 51123 spectra/s] 0.9s | remapping alternative proteins and postprocessing 0.4 s 002. 0002-231030-A1-THY-diaumpire.mzML 0.7 s | deisotoping 0.0 s [progress: 22433/22433 (100%) - 98390 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 003. 0003-231030-B1-THY-diaumpire.mzML 0.8 s | deisotoping 0.1 s [progress: 30269/30269 (100%) - 85748 spectra/s] 0.4s | remapping alternative proteins and postprocessing 0.1 s 004. 0012-23125-A1-SAA-diaumpire.mzML 1.0 s | deisotoping 0.1 s [progress: 38373/38373 (100%) - 112202 spectra/s] 0.3s | remapping alternative proteins and postprocessing 0.1 s 005. 0014-23125-B1-ALL-diaumpire.mzML 0.9 s | deisotoping 0.1 s [progress: 32424/32424 (100%) - 139759 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 006. 0016-23125-A1-ALL-diaumpire.mzML 1.3 s | deisotoping 0.1 s [progress: 48949/48949 (100%) - 106180 spectra/s] 0.5s | remapping alternative proteins and postprocessing 0.1 s ***************************MAIN SEARCH DONE IN 0.201 MIN*************************** *******************************TOTAL TIME 0.268 MIN******************************** INFO: Writing results to output directory 'F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output'. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0001-231030-A1-LT2-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:35 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0001-231030-A1-LT2-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 246 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 237 positives and 9 negatives, size ratio=26.3333 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 3 as initial direction. Could separate 152 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 128 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 8 as initial direction. Could separate 127 training set positives with q<0.01 in that direction. INFO: Found 146 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0710 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 237 PSMs with q<0.05 INFO: Iteration 2: Estimated 237 PSMs with q<0.05 INFO: Iteration 3: Estimated 237 PSMs with q<0.05 INFO: Iteration 4: Estimated 236 PSMs with q<0.05 INFO: Iteration 5: Estimated 233 PSMs with q<0.05 INFO: Iteration 6: Estimated 233 PSMs with q<0.05 INFO: Iteration 7: Estimated 233 PSMs with q<0.05 INFO: Iteration 8: Estimated 233 PSMs with q<0.05 INFO: Iteration 9: Estimated 233 PSMs with q<0.05 INFO: Iteration 10: Estimated 233 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -0.0881 0.1606 -0.0336 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.7835 -0.2206 -0.0584 abs_ppm INFO: 0.0435 -0.6175 -0.6383 isotope_errors INFO: 0.2156 -0.3152 -0.1369 log10_evalue INFO: -0.1227 0.1582 0.1313 hyperscore INFO: -0.1336 0.0752 0.1502 delta_hyperscore INFO: 0.6829 0.5614 0.2399 matched_ion_num INFO: 0.1242 -0.2987 -0.0647 complementary_ions INFO: 0.3770 0.6510 0.3396 ion_series INFO: -0.1100 -0.0783 -0.2689 weighted_average_abs_fragment_ppm INFO: 0.9003 0.6678 0.0365 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: 0.0470 0.1007 0.1251 Charge2 INFO: -0.0396 -0.0760 -0.1557 Charge3 INFO: -0.0341 -0.1088 0.1142 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 1.0688 1.2017 1.0913 m0 INFO: Found 155 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 237 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 143 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 3.9200 cpu seconds or 4 seconds wall clock time. INFO: Elapsed time: 4.11 s INFO: Finished crux percolator. INFO: Return Code:0 Existing files will be overwritten. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0002-231030-A1-THY-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:39 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0002-231030-A1-THY-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 244 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 238 positives and 6 negatives, size ratio=39.6667 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 6 as initial direction. Could separate 135 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 142 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 11 as initial direction. Could separate 161 training set positives with q<0.01 in that direction. INFO: Found 230 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0680 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 238 PSMs with q<0.05 INFO: Iteration 2: Estimated 238 PSMs with q<0.05 INFO: Iteration 3: Estimated 238 PSMs with q<0.05 INFO: Iteration 4: Estimated 238 PSMs with q<0.05 INFO: Iteration 5: Estimated 238 PSMs with q<0.05 INFO: Iteration 6: Estimated 238 PSMs with q<0.05 INFO: Iteration 7: Estimated 238 PSMs with q<0.05 INFO: Iteration 8: Estimated 238 PSMs with q<0.05 INFO: Iteration 9: Estimated 238 PSMs with q<0.05 INFO: Iteration 10: Estimated 238 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -0.2203 0.0472 -0.4316 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.0437 -0.2048 0.2643 abs_ppm INFO: -0.5347 0.0503 -0.2790 isotope_errors INFO: 0.2040 0.2692 -0.1758 log10_evalue INFO: -0.1654 -0.2380 0.1971 hyperscore INFO: -0.2001 -0.2873 0.1511 delta_hyperscore INFO: 0.0625 0.3289 0.2194 matched_ion_num INFO: 0.2661 0.1817 -0.3733 complementary_ions INFO: 0.8275 0.5962 -0.0311 ion_series INFO: 0.0747 -0.6389 -0.3007 weighted_average_abs_fragment_ppm INFO: 1.1822 1.0301 0.0545 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: -0.0315 0.1563 0.0992 Charge2 INFO: 0.0468 -0.1452 -0.0867 Charge3 INFO: -0.0809 -0.0705 -0.0744 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 1.2607 1.0982 1.1598 m0 INFO: Found 236 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 238 target PSMs and 6 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 147 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 2.0690 cpu seconds or 2 seconds wall clock time. INFO: Elapsed time: 2.24 s INFO: Finished crux percolator. INFO: Return Code:0 Existing files will be overwritten. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0003-231030-B1-THY-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:42 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0003-231030-B1-THY-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 173 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 164 positives and 9 negatives, size ratio=18.2222 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 8 as initial direction. Could separate 86 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 86 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 10 as initial direction. Could separate 88 training set positives with q<0.01 in that direction. INFO: Found 136 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0660 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 163 PSMs with q<0.05 INFO: Iteration 2: Estimated 162 PSMs with q<0.05 INFO: Iteration 3: Estimated 162 PSMs with q<0.05 INFO: Iteration 4: Estimated 162 PSMs with q<0.05 INFO: Iteration 5: Estimated 162 PSMs with q<0.05 INFO: Iteration 6: Estimated 162 PSMs with q<0.05 INFO: Iteration 7: Estimated 162 PSMs with q<0.05 INFO: Iteration 8: Estimated 162 PSMs with q<0.05 INFO: Iteration 9: Estimated 162 PSMs with q<0.05 INFO: Iteration 10: Estimated 162 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.7251 0.5315 0.4096 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.1975 -0.2729 -0.2699 abs_ppm INFO: -0.5333 -0.4389 -0.6304 isotope_errors INFO: 0.1482 -0.2322 -0.1027 log10_evalue INFO: -0.1667 -0.2261 0.0515 hyperscore INFO: -0.1611 -0.2200 0.0563 delta_hyperscore INFO: 0.4926 0.5587 0.1046 matched_ion_num INFO: -0.0414 -0.2424 -0.4286 complementary_ions INFO: 0.6378 0.5507 0.2577 ion_series INFO: 0.0389 0.2457 -0.2661 weighted_average_abs_fragment_ppm INFO: 0.2895 0.3133 -0.0180 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: -0.2181 -0.1248 -0.0738 Charge2 INFO: 0.2181 0.1248 0.0738 Charge3 INFO: 0.0000 0.0000 0.0000 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 0.9367 1.0039 0.8679 m0 INFO: Found 162 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 164 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 93 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 6.1100 cpu seconds or 6 seconds wall clock time. INFO: Elapsed time: 6.28 s INFO: Finished crux percolator. INFO: Return Code:0 Existing files will be overwritten. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0012-23125-A1-SAA-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:48 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0012-23125-A1-SAA-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 269 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 262 positives and 7 negatives, size ratio=37.4286 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 4 as initial direction. Could separate 169 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 145 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 5 as initial direction. Could separate 160 training set positives with q<0.01 in that direction. INFO: Found 262 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0670 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 262 PSMs with q<0.05 INFO: Iteration 2: Estimated 262 PSMs with q<0.05 INFO: Iteration 3: Estimated 262 PSMs with q<0.05 INFO: Iteration 4: Estimated 262 PSMs with q<0.05 INFO: Iteration 5: Estimated 262 PSMs with q<0.05 INFO: Iteration 6: Estimated 262 PSMs with q<0.05 INFO: Iteration 7: Estimated 262 PSMs with q<0.05 INFO: Iteration 8: Estimated 262 PSMs with q<0.05 INFO: Iteration 9: Estimated 262 PSMs with q<0.05 INFO: Iteration 10: Estimated 262 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.4735 -0.4970 -0.6124 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.1632 -0.2218 -0.0737 abs_ppm INFO: -0.5193 -0.5651 -0.5351 isotope_errors INFO: 0.2073 -0.0963 -0.1840 log10_evalue INFO: -0.1603 0.0878 0.2093 hyperscore INFO: -0.2048 -0.0202 0.1038 delta_hyperscore INFO: 0.6241 0.8261 0.4388 matched_ion_num INFO: -0.2060 -0.1439 -0.0073 complementary_ions INFO: 0.7315 0.3208 -0.6538 ion_series INFO: 0.2593 0.0388 -0.1948 weighted_average_abs_fragment_ppm INFO: 0.5968 1.0848 0.5347 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: -0.0169 -0.0760 -0.0639 Charge2 INFO: 0.0291 0.0875 0.0747 Charge3 INFO: -0.0807 -0.0737 -0.0692 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 1.3214 1.2065 1.1334 m0 INFO: Found 262 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 262 target PSMs and 7 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 192 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 5.1270 cpu seconds or 6 seconds wall clock time. INFO: Elapsed time: 5.3 s INFO: Finished crux percolator. INFO: Return Code:0 Existing files will be overwritten. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0014-23125-B1-ALL-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:54 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0014-23125-B1-ALL-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 231 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 229 positives and 2 negatives, size ratio=114.5 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 3 as initial direction. Could separate 150 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 1 as initial direction. Could separate 153 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 1 as initial direction. Could separate 153 training set positives with q<0.01 in that direction. INFO: Found 229 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0700 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 229 PSMs with q<0.05 INFO: Iteration 2: Estimated 229 PSMs with q<0.05 INFO: Iteration 3: Estimated 229 PSMs with q<0.05 INFO: Iteration 4: Estimated 229 PSMs with q<0.05 INFO: Iteration 5: Estimated 229 PSMs with q<0.05 INFO: Iteration 6: Estimated 229 PSMs with q<0.05 INFO: Iteration 7: Estimated 229 PSMs with q<0.05 INFO: Iteration 8: Estimated 229 PSMs with q<0.05 INFO: Iteration 9: Estimated 229 PSMs with q<0.05 INFO: Iteration 10: Estimated 229 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: -0.2598 -0.4249 0.2913 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.4921 -0.2923 -0.2618 abs_ppm INFO: 0.3648 0.3277 -0.0761 isotope_errors INFO: -0.1924 -0.0989 0.0156 log10_evalue INFO: 0.1972 0.2269 -0.0183 hyperscore INFO: 0.0915 0.2304 0.0153 delta_hyperscore INFO: 0.4533 0.4662 0.0267 matched_ion_num INFO: -0.6140 -0.7796 -0.1193 complementary_ions INFO: 0.3565 0.3445 0.0438 ion_series INFO: -0.0805 0.0696 -0.0304 weighted_average_abs_fragment_ppm INFO: 0.0266 -0.0640 0.0837 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: 0.0546 -0.0943 0.2132 Charge2 INFO: -0.0546 0.0943 -0.2132 Charge3 INFO: 0.0000 0.0000 0.0000 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 1.1590 1.2136 1.0644 m0 INFO: Found 229 test set PSMs with q<0.05. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 229 target PSMs and 2 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 165 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 1.3620 cpu seconds or 1 seconds wall clock time. INFO: Elapsed time: 1.54 s INFO: Finished crux percolator. INFO: Return Code:0 Existing files will be overwritten. INFO: CPU: LAPTOP-KAC6ORC5 INFO: Crux version: 4.1 INFO: Wed 02/21/2024 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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.peptides.txt --decoy-results-peptides F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.decoy.peptides.txt --results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\crux-output/percolator.target.psms.txt --decoy-results-psms F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\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 F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0016-23125-A1-ALL-diaumpire.fixed.pin INFO: Started Wed Feb 21 22:41:56 2024 INFO: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 INFO: Reading tab-delimited input from datafile F:\bugs\wphipps5\mzml_and_fasta_wphipps5\mzml_and_fasta\0016-23125-A1-ALL-diaumpire.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 group_1 group_2 group_3 group_other INFO: Found 232 PSMs INFO: Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. INFO: Train/test set contains 224 positives and 8 negatives, size ratio=28 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 5 as initial direction. Could separate 119 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 123 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 5 as initial direction. Could separate 132 training set positives with q<0.01 in that direction. INFO: Found 210 test set positives with q<0.05 in initial direction INFO: Reading in data and feature calculation took 0.0680 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 219 PSMs with q<0.05 INFO: Iteration 2: Estimated 223 PSMs with q<0.05 INFO: Iteration 3: Estimated 223 PSMs with q<0.05 INFO: Iteration 4: Estimated 223 PSMs with q<0.05 INFO: Iteration 5: Estimated 223 PSMs with q<0.05 INFO: Iteration 6: Estimated 223 PSMs with q<0.05 INFO: Iteration 7: Estimated 223 PSMs with q<0.05 INFO: Iteration 8: Estimated 223 PSMs with q<0.05 INFO: Iteration 9: Estimated 223 PSMs with q<0.05 INFO: Iteration 10: Estimated 223 PSMs with q<0.05 INFO: Learned normalized SVM weights for the 3 cross-validation splits: INFO: Split1 Split2 Split3 FeatureName INFO: 0.2629 -0.3665 0.1165 retentiontime INFO: 0.0000 0.0000 0.0000 rank INFO: -0.3710 -0.0076 -0.2361 abs_ppm INFO: -0.6290 -0.3376 0.1117 isotope_errors INFO: 0.2805 -0.2668 -0.6306 log10_evalue INFO: -0.1156 0.2826 0.6538 hyperscore INFO: -0.1427 0.3237 0.5245 delta_hyperscore INFO: 0.6688 0.5595 0.2509 matched_ion_num INFO: 0.3069 -0.1079 -0.8071 complementary_ions INFO: 0.6476 0.6428 0.1895 ion_series INFO: 0.0108 0.4129 -0.1034 weighted_average_abs_fragment_ppm INFO: 0.8212 0.2349 -0.1184 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: -0.1165 -0.2081 -0.2704 Charge2 INFO: 0.1228 0.2666 0.2805 Charge3 INFO: -0.0073 -0.1555 -0.0033 Charge4 INFO: 0.0000 0.0000 0.0000 Charge5 INFO: 0.0000 0.0000 0.0000 Charge6 INFO: 0.0000 0.0000 0.0000 Charge7 INFO: 0.0000 0.0000 0.0000 group_1 INFO: 0.0000 0.0000 0.0000 group_2 INFO: 0.0000 0.0000 0.0000 group_3 INFO: 0.0000 0.0000 0.0000 group_other INFO: 1.2353 1.1739 1.2882 m0 INFO: Found 203 test set PSMs with q<0.05. INFO: Less identifications (203 vs 210) after percolator processing than before processing INFO: Resetting score vector, using default vector. Use --override flag to prevent this. INFO: Split 1: Selected feature 5 as initial direction. Could separate 119 training set positives with q<0.01 in that direction. INFO: Split 2: Selected feature 8 as initial direction. Could separate 123 training set positives with q<0.01 in that direction. INFO: Split 3: Selected feature 5 as initial direction. Could separate 132 training set positives with q<0.01 in that direction. INFO: Selected best-scoring PSM per scan+expMass (target-decoy competition): 224 target PSMs and 8 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 109 target peptides with q<0.05. INFO: Calculating posterior error probabilities (PEPs). INFO: Processing took 2.6460 cpu seconds or 3 seconds wall clock time. INFO: Elapsed time: 2.82 s INFO: Finished crux percolator. INFO: Return Code:0 Search done.