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Commit f7642e81 authored by Martin Kuhl's avatar Martin Kuhl
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adding ARC

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runs/run1/psmstats/minimal1_log.txt 0 → 100644
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2021-09-08 09:18:22.6418 minimal1 TRACE Input file: /YDHsjM/psm/minimal1.psm
2021-09-08 09:18:22.6538 minimal1 TRACE Output directory: /YDHsjM/psmstats
2021-09-08 09:18:22.6638 minimal1 TRACE Parameters: { Threshold = Fixed { SequestLike = 5.0
Andromeda = 40.0 }
FastaHeaderToName = <fun:parseProteinIdUsing@177>
KeepTemporaryFiles = true }
2021-09-08 09:18:22.6686 minimal1 TRACE Now performing peptide spectrum matching: /YDHsjM/psm/minimal1.psm Results will be written to: /YDHsjM/psmstats
2021-09-08 09:18:22.6782 minimal1 TRACE outFilePath:/YDHsjM/psmstats/minimal1.qpsm
2021-09-08 09:18:22.6782 minimal1 TRACE plotDirectory:/YDHsjM/psmstats/minimal1_plots
2021-09-08 09:18:22.6782 minimal1 TRACE Copy peptide DB into Memory
2021-09-08 09:18:22.7082 minimal1 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:22.7082 minimal1 TRACE Read scored PSMs.
2021-09-08 09:18:22.7426 minimal1 TRACE Read scored PSMs: finished
2021-09-08 09:18:22.7534 minimal1 TRACE Prepare processing functions.
2021-09-08 09:18:22.7592 minimal1 TRACE Finished preparing processing functions.
2021-09-08 09:18:22.7788 minimal1 TRACE Number of results: 3
runs/run1/psmstats/minimal2.qpsm 0 → 100644
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PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext ModelScore QValue PEPValue StringSequence ProteinNames
sample=1 period=1 cycle=2033 experiment=4 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 0 8.635639049 0 0.6779896705 112.3264921 0 0.7657267969 45.72186797 0 0.5594493789 NaN NaN NaN ILVGDIK Cre02.g143307.t1.1
sample=1 period=1 cycle=2043 experiment=5 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 0 7.816376209 0 0.8192994029 74.99645487 0 1 29.37298389 0 0.7506817907 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
sample=1 period=1 cycle=2038 experiment=7 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 0 7.830779576 0 0.7970537368 112.937008 0 0.8973792939 47.98049859 0 0.6070363597 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
runs/run1/psmstats/minimal2_log.txt 0 → 100644
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2021-09-08 09:18:22.8008 minimal2 TRACE Input file: /YDHsjM/psm/minimal2.psm
2021-09-08 09:18:22.8084 minimal2 TRACE Output directory: /YDHsjM/psmstats
2021-09-08 09:18:22.8084 minimal2 TRACE Parameters: { Threshold = Fixed { SequestLike = 5.0
Andromeda = 40.0 }
FastaHeaderToName = <fun:parseProteinIdUsing@177>
KeepTemporaryFiles = true }
2021-09-08 09:18:22.8084 minimal2 TRACE Now performing peptide spectrum matching: /YDHsjM/psm/minimal2.psm Results will be written to: /YDHsjM/psmstats
2021-09-08 09:18:22.8235 minimal2 TRACE outFilePath:/YDHsjM/psmstats/minimal2.qpsm
2021-09-08 09:18:22.8263 minimal2 TRACE plotDirectory:/YDHsjM/psmstats/minimal2_plots
2021-09-08 09:18:22.8263 minimal2 TRACE Copy peptide DB into Memory
2021-09-08 09:18:22.8263 minimal2 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:22.8367 minimal2 TRACE Read scored PSMs.
2021-09-08 09:18:22.8367 minimal2 TRACE Read scored PSMs: finished
2021-09-08 09:18:22.8478 minimal2 TRACE Prepare processing functions.
2021-09-08 09:18:22.8478 minimal2 TRACE Finished preparing processing functions.
2021-09-08 09:18:22.8478 minimal2 TRACE Number of results: 3
runs/run1/psmstats/minimal3.qpsm 0 → 100644
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PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext ModelScore QValue PEPValue StringSequence ProteinNames
sample=1 period=1 cycle=2033 experiment=4 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 0 8.635639049 0 0.6779896705 112.3264921 0 0.7657267969 45.72186797 0 0.5594493789 NaN NaN NaN ILVGDIK Cre02.g143307.t1.1
sample=1 period=1 cycle=2043 experiment=5 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 0 7.816376209 0 0.8192994029 74.99645487 0 1 29.37298389 0 0.7506817907 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
sample=1 period=1 cycle=2038 experiment=7 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 0 7.830779576 0 0.7970537368 112.937008 0 0.8973792939 47.98049859 0 0.6070363597 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
runs/run1/psmstats/minimal3_log.txt 0 → 100644
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2021-09-08 09:18:22.8662 minimal3 TRACE Input file: /YDHsjM/psm/minimal3.psm
2021-09-08 09:18:22.8662 minimal3 TRACE Output directory: /YDHsjM/psmstats
2021-09-08 09:18:22.8778 minimal3 TRACE Parameters: { Threshold = Fixed { SequestLike = 5.0
Andromeda = 40.0 }
FastaHeaderToName = <fun:parseProteinIdUsing@177>
KeepTemporaryFiles = true }
2021-09-08 09:18:22.8778 minimal3 TRACE Now performing peptide spectrum matching: /YDHsjM/psm/minimal3.psm Results will be written to: /YDHsjM/psmstats
2021-09-08 09:18:22.8894 minimal3 TRACE outFilePath:/YDHsjM/psmstats/minimal3.qpsm
2021-09-08 09:18:22.8894 minimal3 TRACE plotDirectory:/YDHsjM/psmstats/minimal3_plots
2021-09-08 09:18:22.8894 minimal3 TRACE Copy peptide DB into Memory
2021-09-08 09:18:22.8998 minimal3 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:22.8998 minimal3 TRACE Read scored PSMs.
2021-09-08 09:18:22.9109 minimal3 TRACE Read scored PSMs: finished
2021-09-08 09:18:22.9109 minimal3 TRACE Prepare processing functions.
2021-09-08 09:18:22.9167 minimal3 TRACE Finished preparing processing functions.
2021-09-08 09:18:22.9167 minimal3 TRACE Number of results: 3
runs/run1/psmstats/minimal4.qpsm 0 → 100644
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PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext ModelScore QValue PEPValue StringSequence ProteinNames
sample=1 period=1 cycle=2033 experiment=4 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 0 8.635639049 0 0.6779896705 112.3264921 0 0.7657267969 45.72186797 0 0.5594493789 NaN NaN NaN ILVGDIK Cre02.g143307.t1.1
sample=1 period=1 cycle=2043 experiment=5 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 0 7.816376209 0 0.8192994029 74.99645487 0 1 29.37298389 0 0.7506817907 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
sample=1 period=1 cycle=2038 experiment=7 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 0 7.830779576 0 0.7970537368 112.937008 0 0.8973792939 47.98049859 0 0.6070363597 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1
runs/run1/psmstats/minimal4_log.txt 0 → 100644
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2021-09-08 09:18:22.9342 minimal4 TRACE Input file: /YDHsjM/psm/minimal4.psm
2021-09-08 09:18:22.9420 minimal4 TRACE Output directory: /YDHsjM/psmstats
2021-09-08 09:18:22.9459 minimal4 TRACE Parameters: { Threshold = Fixed { SequestLike = 5.0
Andromeda = 40.0 }
FastaHeaderToName = <fun:parseProteinIdUsing@177>
KeepTemporaryFiles = true }
2021-09-08 09:18:22.9459 minimal4 TRACE Now performing peptide spectrum matching: /YDHsjM/psm/minimal4.psm Results will be written to: /YDHsjM/psmstats
2021-09-08 09:18:22.9581 minimal4 TRACE outFilePath:/YDHsjM/psmstats/minimal4.qpsm
2021-09-08 09:18:22.9581 minimal4 TRACE plotDirectory:/YDHsjM/psmstats/minimal4_plots
2021-09-08 09:18:22.9581 minimal4 TRACE Copy peptide DB into Memory
2021-09-08 09:18:22.9696 minimal4 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:22.9696 minimal4 TRACE Read scored PSMs.
2021-09-08 09:18:22.9815 minimal4 TRACE Read scored PSMs: finished
2021-09-08 09:18:22.9815 minimal4 TRACE Prepare processing functions.
2021-09-08 09:18:22.9882 minimal4 TRACE Finished preparing processing functions.
2021-09-08 09:18:22.9882 minimal4 TRACE Number of results: 3
runs/run1/psmstats/minimal_log.txt 0 → 100644
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2021-09-07 09:57:28.3987 minimal TRACE Input file: /FuNLno/psm/minimal.psm
2021-09-07 09:57:28.4081 minimal TRACE Output directory: /FuNLno/psmstats
2021-09-07 09:57:28.4191 minimal TRACE Parameters: { Threshold = Fixed { SequestLike = 5.0
Andromeda = 40.0 }
FastaHeaderToName = <fun:parseProteinIdUsing@177>
KeepTemporaryFiles = true }
2021-09-07 09:57:28.4191 minimal TRACE Now performing peptide spectrum matching: /FuNLno/psm/minimal.psm Results will be written to: /FuNLno/psmstats
2021-09-07 09:57:28.4373 minimal TRACE outFilePath:/FuNLno/psmstats/minimal.qpsm
2021-09-07 09:57:28.4373 minimal TRACE plotDirectory:/FuNLno/psmstats/minimal_plots
2021-09-07 09:57:28.4373 minimal TRACE Copy peptide DB into Memory
2021-09-07 09:57:28.4731 minimal TRACE Copy peptide DB into Memory: finished
2021-09-07 09:57:28.4769 minimal TRACE Read scored PSMs.
2021-09-07 09:57:28.5118 minimal TRACE Read scored PSMs: finished
2021-09-07 09:57:28.5118 minimal TRACE Prepare processing functions.
2021-09-07 09:57:28.5231 minimal TRACE Finished preparing processing functions.
2021-09-07 09:57:28.5456 minimal TRACE Number of results: 3
runs/run1/psmstats/pSMStatisticsParamsFixed.json 0 → 100644
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{"Threshold":{"Case":"Fixed","Fields":[{"SequestLike":5.0,"Andromeda":40.0}]},"ParseProteinIDRegexPattern":"id","KeepTemporaryFiles":true}
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runs/run1/quant/PSMBasedQuantification_log.txt 0 → 100644
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2021-09-08 09:18:27.1279 PSMBasedQuantification TRACE CLIArguments: [InstrumentOutput ["/YDHsjM/dataset"]; ScoredPSMs ["/YDHsjM/psmstats"];
PeptideDataBase
"/var/lib/cwl/stg033e2d36-2b0e-4346-8375-7b9f00359e05/Minimal.db";
ParamFile
"/var/lib/cwl/stg28f52b17-3960-4d8f-b044-98facf9de364/QuantificationParams.json";
OutputDirectory "quant"; Parallelism_Level 1]
2021-09-08 09:18:27.2974 PSMBasedQuantification TRACE Database found at given location (/var/lib/cwl/stg033e2d36-2b0e-4346-8375-7b9f00359e05/Minimal.db)
2021-09-08 09:18:27.3782 PSMBasedQuantification TRACE Set Index on data base if not present.
2021-09-08 09:18:27.4049 PSMBasedQuantification TRACE Set Index on data base if not present: finished
2021-09-08 09:18:27.4266 PSMBasedQuantification TRACE mz files : [|"/YDHsjM/dataset/minimal1.mzlite"; "/YDHsjM/dataset/minimal2.mzlite";
"/YDHsjM/dataset/minimal3.mzlite"; "/YDHsjM/dataset/minimal4.mzlite"|]
2021-09-08 09:18:27.4266 PSMBasedQuantification TRACE PEP files : [|"/YDHsjM/psmstats/minimal1.qpsm"; "/YDHsjM/psmstats/minimal2.qpsm";
"/YDHsjM/psmstats/minimal3.qpsm"; "/YDHsjM/psmstats/minimal4.qpsm"|]
2021-09-08 09:18:27.4415 PSMBasedQuantification TRACE Program is running on 1 cores
runs/run1/quant/QuantificationParams.json 0 → 100644
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{"PerformLabeledQuantification":true,"XicExtraction":{"ScanTimeWindow":2.0,"MzWindow_Da":{"Case":"Fixed","Fields":[0.7]},"XicProcessing":{"Case":"Wavelet","Fields":[{"Borderpadding":null,"BorderPadMethod":{"Case":"Random"},"InternalPaddingMethod":{"Case":"LinearInterpolation"},"HugeGapPaddingMethod":{"Case":"Zero"},"HugeGapPaddingDistance":100.0,"MinPeakDistance":null,"MinPeakLength":{"Case":"Some","Fields":[0.1]},"MaxPeakLength":1.5,"NoiseQuantile":0.01,"MinSNR":0.01}]},"TopKPSMs":null},"BaseLineCorrection":{"Case":"Some","Fields":[{"MaxIterations":10,"Lambda":6,"P":0.05}]}}
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runs/run1/quant/minimal.quant 0 → 100644
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StringSequence GlobalMod Charge PepSequenceID ModSequenceID PrecursorMZ MeasuredMass TheoMass AbsDeltaMass MeanPercolatorScore QValue PEPValue ProteinNames QuantMz_Light Quant_Light MeasuredApex_Light Seo_Light Params_Light Difference_SearchRT_FittedRT_Light KLDiv_Observed_Theoretical_Light KLDiv_CorrectedObserved_Theoretical_Light QuantMz_Heavy Quant_Heavy MeasuredApex_Heavy Seo_Heavy Params_Heavy Difference_SearchRT_FittedRT_Heavy KLDiv_Observed_Theoretical_Heavy KLDiv_CorrectedObserved_Theoretical_Heavy Correlation_Light_Heavy QuantificationSource IsotopicPatternMz_Light IsotopicPatternIntensity_Observed_Light IsotopicPatternIntensity_Corrected_Light RtTrace_Light IntensityTrace_Observed_Light IntensityTrace_Corrected_Light IsotopicPatternMz_Heavy IsotopicPatternIntensity_Observed_Heavy IsotopicPatternIntensity_Corrected_Heavy RtTrace_Heavy IntensityTrace_Observed_Heavy IntensityTrace_Corrected_Heavy
ILVGDIK 1 2 4 8 383.22785456403994 764.4411561944598 764.4508194280799 0.009663233620017309 NaN NaN NaN Cre02.g143307.t1.1 379.23971499043995 13895.47339654926 73151.81512271758 4553.5228365421535 80403.83902787043;32.81183757130164;0.06894561144220064 -0.049771102470330675 0 0 383.22785456403994 185047.80944265015 1289631.2384404598 31578.07166840622 1676520.6094317106;32.76206646883131;0.04403369375063307;0.04506675900528934 0.2328335311686942 0.0010312303213717532 0.0030055184355344128 0.9740607001469397 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 3877.126953125;9682.626953125;17809.18359375;28699.48828125;32246.203125;50208.08203125;76544.65625;93217.671875;82655.2109375;55049.8203125;35156.421875;17798.73828125;8638.1083984375;5820.25341796875;3716.79736328125;5644.71337890625;7111.89306640625;7335.0400390625;9308.017578125;10591.529296875;12635.1689453125;227.0161590576172;2370.625244140625;15502.4716796875;10774.1435546875;193.37698364257812;35.557044982910156;8247.81640625 0;0;5470.768434920141;16833.46277756074;20852.59975355943;39286.94406141986;66096.0367007657;83241.6315506234;73151.81512271758;46019.134610441266;26598.508549596754;9713.653956279584;1025.9027275973722;0;0;0;1391.5567352333428;2087.734726962194;4533.762339051596;6290.340080095969;8807.058368720365;0;0;13093.637482286453;8838.408768565765;0;0;7731.385309588123 383.2310364702693;383.73250408075376 0.7404942145944616;0.25950578540553837 0.7546039625226236;0.2453960374773764 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 401.9676818847656;1605.35009765625;7275.984375;59889.515625;262159.59375;736966.75;1274451.125;1334963;942810.6875;526645.4375;253429.359375;119654.5390625;52576.61328125;27701.771484375;17402.494140625;11673.9638671875;9211.7109375;7015.09228515625;6758.97314453125;4151.7490234375;8389.21484375;7029.37109375;6080.73486328125;6686.37841796875;4900.3876953125;4916.0078125;3702.856689453125;4123.65771484375 0;0;0;5129.602796132713;209755.8382364536;686919.6445741121;1226761.3123641082;1289631.2384404598;899837.7895491186;486032.2054544751;215176.5403040297;83762.80050617293;19046.532491718164;0;0;0;0;0;0;0;0;0;0;0;0;2106.4631377189044;3256.680682980992;6040.850074638076
ALEVIPR 0 2 22 87 399.24278899524 796.47102505686 796.48068829048 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 0.06758842550379995 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 0.03236152238286394 5.9251385491228964E-05 0.003031633208957475 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.23055482892653;404.7317573195174 0.7202677937323957;0.27973220626760437 0.7500448933950046;0.24995510660499548 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
ALEVIPR 1 2 22 88 404.22796346224 806.4413739908599 806.4510372244799 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 -0.03236152238286394 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 -0.08088338211333479 0 0 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.2304659161266 1 1 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
runs/run1/quant/minimal1.quant 0 → 100644
+ 4
− 0
View file @ f7642e81
StringSequence GlobalMod Charge PepSequenceID ModSequenceID PrecursorMZ MeasuredMass TheoMass AbsDeltaMass MeanPercolatorScore QValue PEPValue ProteinNames QuantMz_Light Quant_Light MeasuredApex_Light Seo_Light Params_Light Difference_SearchRT_FittedRT_Light KLDiv_Observed_Theoretical_Light KLDiv_CorrectedObserved_Theoretical_Light QuantMz_Heavy Quant_Heavy MeasuredApex_Heavy Seo_Heavy Params_Heavy Difference_SearchRT_FittedRT_Heavy KLDiv_Observed_Theoretical_Heavy KLDiv_CorrectedObserved_Theoretical_Heavy Correlation_Light_Heavy QuantificationSource IsotopicPatternMz_Light IsotopicPatternIntensity_Observed_Light IsotopicPatternIntensity_Corrected_Light RtTrace_Light IntensityTrace_Observed_Light IntensityTrace_Corrected_Light IsotopicPatternMz_Heavy IsotopicPatternIntensity_Observed_Heavy IsotopicPatternIntensity_Corrected_Heavy RtTrace_Heavy IntensityTrace_Observed_Heavy IntensityTrace_Corrected_Heavy
ILVGDIK 1 2 4 8 383.22785456403994 764.4411561944598 764.4508194280799 0.009663233620017309 NaN NaN NaN Cre02.g143307.t1.1 379.23971499043995 13895.47339654926 73151.81512271758 4553.5228365421535 80403.83902787043;32.81183757130164;0.06894561144220064 -0.049771102470330675 0 0 383.22785456403994 185047.80944265015 1289631.2384404598 31578.07166840622 1676520.6094317106;32.76206646883131;0.04403369375063307;0.04506675900528934 0.2328335311686942 0.0010312303213717532 0.0030055184355344128 0.9740607001469397 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 3877.126953125;9682.626953125;17809.18359375;28699.48828125;32246.203125;50208.08203125;76544.65625;93217.671875;82655.2109375;55049.8203125;35156.421875;17798.73828125;8638.1083984375;5820.25341796875;3716.79736328125;5644.71337890625;7111.89306640625;7335.0400390625;9308.017578125;10591.529296875;12635.1689453125;227.0161590576172;2370.625244140625;15502.4716796875;10774.1435546875;193.37698364257812;35.557044982910156;8247.81640625 0;0;5470.768434920141;16833.46277756074;20852.59975355943;39286.94406141986;66096.0367007657;83241.6315506234;73151.81512271758;46019.134610441266;26598.508549596754;9713.653956279584;1025.9027275973722;0;0;0;1391.5567352333428;2087.734726962194;4533.762339051596;6290.340080095969;8807.058368720365;0;0;13093.637482286453;8838.408768565765;0;0;7731.385309588123 383.2310364702693;383.73250408075376 0.7404942145944616;0.25950578540553837 0.7546039625226236;0.2453960374773764 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 401.9676818847656;1605.35009765625;7275.984375;59889.515625;262159.59375;736966.75;1274451.125;1334963;942810.6875;526645.4375;253429.359375;119654.5390625;52576.61328125;27701.771484375;17402.494140625;11673.9638671875;9211.7109375;7015.09228515625;6758.97314453125;4151.7490234375;8389.21484375;7029.37109375;6080.73486328125;6686.37841796875;4900.3876953125;4916.0078125;3702.856689453125;4123.65771484375 0;0;0;5129.602796132713;209755.8382364536;686919.6445741121;1226761.3123641082;1289631.2384404598;899837.7895491186;486032.2054544751;215176.5403040297;83762.80050617293;19046.532491718164;0;0;0;0;0;0;0;0;0;0;0;0;2106.4631377189044;3256.680682980992;6040.850074638076
ALEVIPR 0 2 22 87 399.24278899524 796.47102505686 796.48068829048 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 0.06758842550379995 0 0 404.22796346224 105699.21115950718 535482.9571224969 31861.157774525702 602034.402211528;33.26066936477699;0.07004231682060993 0.03262553971921278 5.9251385491228964E-05 0.003031633208957475 0.9297388842851689 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.23055482892653;404.7317573195174 0.7202677937323957;0.27973220626760437 0.7500448933950046;0.24995510660499548 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
ALEVIPR 1 2 22 88 404.22796346224 806.4413739908599 806.4510372244799 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 -0.03236152238286394 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 -0.08088338211333479 0 0 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.2304659161266 1 1 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
runs/run1/quant/minimal1_log.txt 0 → 100644
+ 46
− 0
View file @ f7642e81
2021-09-08 09:18:27.4593 minimal1 TRACE Input file: /YDHsjM/dataset/minimal1.mzlite
2021-09-08 09:18:27.4705 minimal1 TRACE Output directory: /YDHsjM/quant
2021-09-08 09:18:27.4803 minimal1 TRACE Parameters: { PerformLabeledQuantification = true
XicExtraction =
{ ScanTimeWindow = 2.0
MzWindow_Da = Fixed 0.7
XicProcessing =
Wavelet
{ Borderpadding = None
BorderPadMethod = Random
InternalPaddingMethod =
LinearInterpolation
HugeGapPaddingMethod = Zero
HugeGapPaddingDistance = 100.0
MinPeakDistance = None
MinPeakLength = Some 0.1
MaxPeakLength = 1.5
NoiseQuantile = 0.01
MinSNR = 0.01 }
TopKPSMs = None }
BaseLineCorrection = Some { MaxIterations = 10
Lambda = 6
P = 0.05 } }
2021-09-08 09:18:27.4882 minimal1 TRACE Now performing Quantification using: /YDHsjM/dataset/minimal1.mzlite and /YDHsjM/psmstats/minimal1.qpsm, Results will be written to: /YDHsjM/quant
2021-09-08 09:18:27.4882 minimal1 TRACE outFilePath:/YDHsjM/quant/minimal1.quant
2021-09-08 09:18:27.4998 minimal1 TRACE plotDirectory:/YDHsjM/quant/minimal1_plots
2021-09-08 09:18:27.4998 minimal1 TRACE Copy peptide DB into Memory
2021-09-08 09:18:27.5169 minimal1 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:27.5169 minimal1 TRACE Get peptide lookUp function
2021-09-08 09:18:27.5775 minimal1 TRACE Get peptide lookUp function: finished
2021-09-08 09:18:27.5882 minimal1 TRACE Init connection to mass spectrum data.
2021-09-08 09:18:27.6172 minimal1 TRACE Create RetentionTime index
2021-09-08 09:18:27.7258 minimal1 TRACE Create RetentionTime index:finished
2021-09-08 09:18:27.7258 minimal1 TRACE Read and sort ms1s
2021-09-08 09:18:27.7716 minimal1 TRACE Read and sort ms1s:finished
2021-09-08 09:18:27.7818 minimal1 TRACE Read scored PSMs
2021-09-08 09:18:27.8153 minimal1 TRACE Read scored PSMs:finished
2021-09-08 09:18:27.8234 minimal1 TRACE Estimate precursor mz standard deviation and mz correction.
2021-09-08 09:18:27.8361 minimal1 TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
2021-09-08 09:18:27.8361 minimal1 TRACE init lookup functions
2021-09-08 09:18:27.8475 minimal1 TRACE init lookup functions:finished
2021-09-08 09:18:27.8475 minimal1 TRACE init quantification functions
2021-09-08 09:18:27.8475 minimal1 TRACE init quantification functions:finished
2021-09-08 09:18:27.8561 minimal1 TRACE executing quantification
2021-09-08 09:18:27.8561 minimal1 TRACE 0 peptides quantified
2021-09-08 09:18:28.2720 minimal1 TRACE executing quantification:finished
runs/run1/quant/minimal2.quant 0 → 100644
+ 4
− 0
View file @ f7642e81
StringSequence GlobalMod Charge PepSequenceID ModSequenceID PrecursorMZ MeasuredMass TheoMass AbsDeltaMass MeanPercolatorScore QValue PEPValue ProteinNames QuantMz_Light Quant_Light MeasuredApex_Light Seo_Light Params_Light Difference_SearchRT_FittedRT_Light KLDiv_Observed_Theoretical_Light KLDiv_CorrectedObserved_Theoretical_Light QuantMz_Heavy Quant_Heavy MeasuredApex_Heavy Seo_Heavy Params_Heavy Difference_SearchRT_FittedRT_Heavy KLDiv_Observed_Theoretical_Heavy KLDiv_CorrectedObserved_Theoretical_Heavy Correlation_Light_Heavy QuantificationSource IsotopicPatternMz_Light IsotopicPatternIntensity_Observed_Light IsotopicPatternIntensity_Corrected_Light RtTrace_Light IntensityTrace_Observed_Light IntensityTrace_Corrected_Light IsotopicPatternMz_Heavy IsotopicPatternIntensity_Observed_Heavy IsotopicPatternIntensity_Corrected_Heavy RtTrace_Heavy IntensityTrace_Observed_Heavy IntensityTrace_Corrected_Heavy
ILVGDIK 1 2 4 8 383.22785456403994 764.4411561944598 764.4508194280799 0.009663233620017309 NaN NaN NaN Cre02.g143307.t1.1 379.23971499043995 13895.47339654926 73151.81512271758 4553.5228365421535 80403.83902787043;32.81183757130164;0.06894561144220064 -0.049771102470330675 0 0 383.22785456403994 185047.80944265015 1289631.2384404598 31578.07166840622 1676520.6094317106;32.76206646883131;0.04403369375063307;0.04506675900528934 0.2328335311686942 0.0010312303213717532 0.0030055184355344128 0.9740607001469397 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 3877.126953125;9682.626953125;17809.18359375;28699.48828125;32246.203125;50208.08203125;76544.65625;93217.671875;82655.2109375;55049.8203125;35156.421875;17798.73828125;8638.1083984375;5820.25341796875;3716.79736328125;5644.71337890625;7111.89306640625;7335.0400390625;9308.017578125;10591.529296875;12635.1689453125;227.0161590576172;2370.625244140625;15502.4716796875;10774.1435546875;193.37698364257812;35.557044982910156;8247.81640625 0;0;5470.768434920141;16833.46277756074;20852.59975355943;39286.94406141986;66096.0367007657;83241.6315506234;73151.81512271758;46019.134610441266;26598.508549596754;9713.653956279584;1025.9027275973722;0;0;0;1391.5567352333428;2087.734726962194;4533.762339051596;6290.340080095969;8807.058368720365;0;0;13093.637482286453;8838.408768565765;0;0;7731.385309588123 383.2310364702693;383.73250408075376 0.7404942145944616;0.25950578540553837 0.7546039625226236;0.2453960374773764 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 401.9676818847656;1605.35009765625;7275.984375;59889.515625;262159.59375;736966.75;1274451.125;1334963;942810.6875;526645.4375;253429.359375;119654.5390625;52576.61328125;27701.771484375;17402.494140625;11673.9638671875;9211.7109375;7015.09228515625;6758.97314453125;4151.7490234375;8389.21484375;7029.37109375;6080.73486328125;6686.37841796875;4900.3876953125;4916.0078125;3702.856689453125;4123.65771484375 0;0;0;5129.602796132713;209755.8382364536;686919.6445741121;1226761.3123641082;1289631.2384404598;899837.7895491186;486032.2054544751;215176.5403040297;83762.80050617293;19046.532491718164;0;0;0;0;0;0;0;0;0;0;0;0;2106.4631377189044;3256.680682980992;6040.850074638076
ALEVIPR 0 2 22 87 399.24278899524 796.47102505686 796.48068829048 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 0.06758842550379995 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 0.03236152238286394 5.9251385491228964E-05 0.003031633208957475 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.23055482892653;404.7317573195174 0.7202677937323957;0.27973220626760437 0.7500448933950046;0.24995510660499548 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
ALEVIPR 1 2 22 88 404.22796346224 806.4413739908599 806.4510372244799 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 -0.03236152238286394 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 -0.08088338211333479 0 0 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.2304659161266 1 1 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
runs/run1/quant/minimal2_log.txt 0 → 100644
+ 46
− 0
View file @ f7642e81
2021-09-08 09:18:28.2801 minimal2 TRACE Input file: /YDHsjM/dataset/minimal2.mzlite
2021-09-08 09:18:28.2875 minimal2 TRACE Output directory: /YDHsjM/quant
2021-09-08 09:18:28.2875 minimal2 TRACE Parameters: { PerformLabeledQuantification = true
XicExtraction =
{ ScanTimeWindow = 2.0
MzWindow_Da = Fixed 0.7
XicProcessing =
Wavelet
{ Borderpadding = None
BorderPadMethod = Random
InternalPaddingMethod =
LinearInterpolation
HugeGapPaddingMethod = Zero
HugeGapPaddingDistance = 100.0
MinPeakDistance = None
MinPeakLength = Some 0.1
MaxPeakLength = 1.5
NoiseQuantile = 0.01
MinSNR = 0.01 }
TopKPSMs = None }
BaseLineCorrection = Some { MaxIterations = 10
Lambda = 6
P = 0.05 } }
2021-09-08 09:18:28.2875 minimal2 TRACE Now performing Quantification using: /YDHsjM/dataset/minimal2.mzlite and /YDHsjM/psmstats/minimal2.qpsm, Results will be written to: /YDHsjM/quant
2021-09-08 09:18:28.2982 minimal2 TRACE outFilePath:/YDHsjM/quant/minimal2.quant
2021-09-08 09:18:28.3064 minimal2 TRACE plotDirectory:/YDHsjM/quant/minimal2_plots
2021-09-08 09:18:28.3064 minimal2 TRACE Copy peptide DB into Memory
2021-09-08 09:18:28.3064 minimal2 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:28.3164 minimal2 TRACE Get peptide lookUp function
2021-09-08 09:18:28.3164 minimal2 TRACE Get peptide lookUp function: finished
2021-09-08 09:18:28.3164 minimal2 TRACE Init connection to mass spectrum data.
2021-09-08 09:18:28.3540 minimal2 TRACE Create RetentionTime index
2021-09-08 09:18:28.3876 minimal2 TRACE Create RetentionTime index:finished
2021-09-08 09:18:28.3876 minimal2 TRACE Read and sort ms1s
2021-09-08 09:18:28.4148 minimal2 TRACE Read and sort ms1s:finished
2021-09-08 09:18:28.4235 minimal2 TRACE Read scored PSMs
2021-09-08 09:18:28.4335 minimal2 TRACE Read scored PSMs:finished
2021-09-08 09:18:28.4362 minimal2 TRACE Estimate precursor mz standard deviation and mz correction.
2021-09-08 09:18:28.4362 minimal2 TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
2021-09-08 09:18:28.4362 minimal2 TRACE init lookup functions
2021-09-08 09:18:28.4362 minimal2 TRACE init lookup functions:finished
2021-09-08 09:18:28.4487 minimal2 TRACE init quantification functions
2021-09-08 09:18:28.4487 minimal2 TRACE init quantification functions:finished
2021-09-08 09:18:28.4487 minimal2 TRACE executing quantification
2021-09-08 09:18:28.4578 minimal2 TRACE 0 peptides quantified
2021-09-08 09:18:28.5903 minimal2 TRACE executing quantification:finished
runs/run1/quant/minimal3.quant 0 → 100644
+ 4
− 0
View file @ f7642e81
StringSequence GlobalMod Charge PepSequenceID ModSequenceID PrecursorMZ MeasuredMass TheoMass AbsDeltaMass MeanPercolatorScore QValue PEPValue ProteinNames QuantMz_Light Quant_Light MeasuredApex_Light Seo_Light Params_Light Difference_SearchRT_FittedRT_Light KLDiv_Observed_Theoretical_Light KLDiv_CorrectedObserved_Theoretical_Light QuantMz_Heavy Quant_Heavy MeasuredApex_Heavy Seo_Heavy Params_Heavy Difference_SearchRT_FittedRT_Heavy KLDiv_Observed_Theoretical_Heavy KLDiv_CorrectedObserved_Theoretical_Heavy Correlation_Light_Heavy QuantificationSource IsotopicPatternMz_Light IsotopicPatternIntensity_Observed_Light IsotopicPatternIntensity_Corrected_Light RtTrace_Light IntensityTrace_Observed_Light IntensityTrace_Corrected_Light IsotopicPatternMz_Heavy IsotopicPatternIntensity_Observed_Heavy IsotopicPatternIntensity_Corrected_Heavy RtTrace_Heavy IntensityTrace_Observed_Heavy IntensityTrace_Corrected_Heavy
ILVGDIK 1 2 4 8 383.22785456403994 764.4411561944598 764.4508194280799 0.009663233620017309 NaN NaN NaN Cre02.g143307.t1.1 379.23971499043995 13895.47339654926 73151.81512271758 4553.5228365421535 80403.83902787043;32.81183757130164;0.06894561144220064 -0.049771102470330675 0 0 383.22785456403994 185047.80944265015 1289631.2384404598 31578.07166840622 1676520.6094317106;32.76206646883131;0.04403369375063307;0.04506675900528934 0.2328335311686942 0.0010312303213717532 0.0030055184355344128 0.9740607001469397 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 3877.126953125;9682.626953125;17809.18359375;28699.48828125;32246.203125;50208.08203125;76544.65625;93217.671875;82655.2109375;55049.8203125;35156.421875;17798.73828125;8638.1083984375;5820.25341796875;3716.79736328125;5644.71337890625;7111.89306640625;7335.0400390625;9308.017578125;10591.529296875;12635.1689453125;227.0161590576172;2370.625244140625;15502.4716796875;10774.1435546875;193.37698364257812;35.557044982910156;8247.81640625 0;0;5470.768434920141;16833.46277756074;20852.59975355943;39286.94406141986;66096.0367007657;83241.6315506234;73151.81512271758;46019.134610441266;26598.508549596754;9713.653956279584;1025.9027275973722;0;0;0;1391.5567352333428;2087.734726962194;4533.762339051596;6290.340080095969;8807.058368720365;0;0;13093.637482286453;8838.408768565765;0;0;7731.385309588123 383.2310364702693;383.73250408075376 0.7404942145944616;0.25950578540553837 0.7546039625226236;0.2453960374773764 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 401.9676818847656;1605.35009765625;7275.984375;59889.515625;262159.59375;736966.75;1274451.125;1334963;942810.6875;526645.4375;253429.359375;119654.5390625;52576.61328125;27701.771484375;17402.494140625;11673.9638671875;9211.7109375;7015.09228515625;6758.97314453125;4151.7490234375;8389.21484375;7029.37109375;6080.73486328125;6686.37841796875;4900.3876953125;4916.0078125;3702.856689453125;4123.65771484375 0;0;0;5129.602796132713;209755.8382364536;686919.6445741121;1226761.3123641082;1289631.2384404598;899837.7895491186;486032.2054544751;215176.5403040297;83762.80050617293;19046.532491718164;0;0;0;0;0;0;0;0;0;0;0;0;2106.4631377189044;3256.680682980992;6040.850074638076
ALEVIPR 0 2 22 87 399.24278899524 796.47102505686 796.48068829048 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 0.06758842550379995 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 0.03236152238286394 5.9251385491228964E-05 0.003031633208957475 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.23055482892653;404.7317573195174 0.7202677937323957;0.27973220626760437 0.7500448933950046;0.24995510660499548 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
ALEVIPR 1 2 22 88 404.22796346224 806.4413739908599 806.4510372244799 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 -0.03236152238286394 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 -0.08088338211333479 0 0 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.2304659161266 1 1 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
runs/run1/quant/minimal3_log.txt 0 → 100644
+ 46
− 0
View file @ f7642e81
2021-09-08 09:18:28.5903 minimal3 TRACE Input file: /YDHsjM/dataset/minimal3.mzlite
2021-09-08 09:18:28.6045 minimal3 TRACE Output directory: /YDHsjM/quant
2021-09-08 09:18:28.6086 minimal3 TRACE Parameters: { PerformLabeledQuantification = true
XicExtraction =
{ ScanTimeWindow = 2.0
MzWindow_Da = Fixed 0.7
XicProcessing =
Wavelet
{ Borderpadding = None
BorderPadMethod = Random
InternalPaddingMethod =
LinearInterpolation
HugeGapPaddingMethod = Zero
HugeGapPaddingDistance = 100.0
MinPeakDistance = None
MinPeakLength = Some 0.1
MaxPeakLength = 1.5
NoiseQuantile = 0.01
MinSNR = 0.01 }
TopKPSMs = None }
BaseLineCorrection = Some { MaxIterations = 10
Lambda = 6
P = 0.05 } }
2021-09-08 09:18:28.6086 minimal3 TRACE Now performing Quantification using: /YDHsjM/dataset/minimal3.mzlite and /YDHsjM/psmstats/minimal3.qpsm, Results will be written to: /YDHsjM/quant
2021-09-08 09:18:28.6170 minimal3 TRACE outFilePath:/YDHsjM/quant/minimal3.quant
2021-09-08 09:18:28.6170 minimal3 TRACE plotDirectory:/YDHsjM/quant/minimal3_plots
2021-09-08 09:18:28.6280 minimal3 TRACE Copy peptide DB into Memory
2021-09-08 09:18:28.6280 minimal3 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:28.6367 minimal3 TRACE Get peptide lookUp function
2021-09-08 09:18:28.6367 minimal3 TRACE Get peptide lookUp function: finished
2021-09-08 09:18:28.6367 minimal3 TRACE Init connection to mass spectrum data.
2021-09-08 09:18:28.6636 minimal3 TRACE Create RetentionTime index
2021-09-08 09:18:28.6920 minimal3 TRACE Create RetentionTime index:finished
2021-09-08 09:18:28.6960 minimal3 TRACE Read and sort ms1s
2021-09-08 09:18:28.7190 minimal3 TRACE Read and sort ms1s:finished
2021-09-08 09:18:28.7280 minimal3 TRACE Read scored PSMs
2021-09-08 09:18:28.7422 minimal3 TRACE Read scored PSMs:finished
2021-09-08 09:18:28.7422 minimal3 TRACE Estimate precursor mz standard deviation and mz correction.
2021-09-08 09:18:28.7482 minimal3 TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
2021-09-08 09:18:28.7482 minimal3 TRACE init lookup functions
2021-09-08 09:18:28.7482 minimal3 TRACE init lookup functions:finished
2021-09-08 09:18:28.7572 minimal3 TRACE init quantification functions
2021-09-08 09:18:28.7572 minimal3 TRACE init quantification functions:finished
2021-09-08 09:18:28.7572 minimal3 TRACE executing quantification
2021-09-08 09:18:28.7572 minimal3 TRACE 0 peptides quantified
2021-09-08 09:18:28.9000 minimal3 TRACE executing quantification:finished
runs/run1/quant/minimal4.quant 0 → 100644
+ 4
− 0
View file @ f7642e81
StringSequence GlobalMod Charge PepSequenceID ModSequenceID PrecursorMZ MeasuredMass TheoMass AbsDeltaMass MeanPercolatorScore QValue PEPValue ProteinNames QuantMz_Light Quant_Light MeasuredApex_Light Seo_Light Params_Light Difference_SearchRT_FittedRT_Light KLDiv_Observed_Theoretical_Light KLDiv_CorrectedObserved_Theoretical_Light QuantMz_Heavy Quant_Heavy MeasuredApex_Heavy Seo_Heavy Params_Heavy Difference_SearchRT_FittedRT_Heavy KLDiv_Observed_Theoretical_Heavy KLDiv_CorrectedObserved_Theoretical_Heavy Correlation_Light_Heavy QuantificationSource IsotopicPatternMz_Light IsotopicPatternIntensity_Observed_Light IsotopicPatternIntensity_Corrected_Light RtTrace_Light IntensityTrace_Observed_Light IntensityTrace_Corrected_Light IsotopicPatternMz_Heavy IsotopicPatternIntensity_Observed_Heavy IsotopicPatternIntensity_Corrected_Heavy RtTrace_Heavy IntensityTrace_Observed_Heavy IntensityTrace_Corrected_Heavy
ILVGDIK 1 2 4 8 383.22785456403994 764.4411561944598 764.4508194280799 0.009663233620017309 NaN NaN NaN Cre02.g143307.t1.1 379.23971499043995 13895.47339654926 73151.81512271758 4553.5228365421535 80403.83902787043;32.81183757130164;0.06894561144220064 -0.049771102470330675 0 0 383.22785456403994 185047.80944265015 1289631.2384404598 31578.07166840622 1676520.6094317106;32.76206646883131;0.04403369375063307;0.04506675900528934 0.2328335311686942 0.0010312303213717532 0.0030055184355344128 0.9740607001469397 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 3877.126953125;9682.626953125;17809.18359375;28699.48828125;32246.203125;50208.08203125;76544.65625;93217.671875;82655.2109375;55049.8203125;35156.421875;17798.73828125;8638.1083984375;5820.25341796875;3716.79736328125;5644.71337890625;7111.89306640625;7335.0400390625;9308.017578125;10591.529296875;12635.1689453125;227.0161590576172;2370.625244140625;15502.4716796875;10774.1435546875;193.37698364257812;35.557044982910156;8247.81640625 0;0;5470.768434920141;16833.46277756074;20852.59975355943;39286.94406141986;66096.0367007657;83241.6315506234;73151.81512271758;46019.134610441266;26598.508549596754;9713.653956279584;1025.9027275973722;0;0;0;1391.5567352333428;2087.734726962194;4533.762339051596;6290.340080095969;8807.058368720365;0;0;13093.637482286453;8838.408768565765;0;0;7731.385309588123 383.2310364702693;383.73250408075376 0.7404942145944616;0.25950578540553837 0.7546039625226236;0.2453960374773764 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 401.9676818847656;1605.35009765625;7275.984375;59889.515625;262159.59375;736966.75;1274451.125;1334963;942810.6875;526645.4375;253429.359375;119654.5390625;52576.61328125;27701.771484375;17402.494140625;11673.9638671875;9211.7109375;7015.09228515625;6758.97314453125;4151.7490234375;8389.21484375;7029.37109375;6080.73486328125;6686.37841796875;4900.3876953125;4916.0078125;3702.856689453125;4123.65771484375 0;0;0;5129.602796132713;209755.8382364536;686919.6445741121;1226761.3123641082;1289631.2384404598;899837.7895491186;486032.2054544751;215176.5403040297;83762.80050617293;19046.532491718164;0;0;0;0;0;0;0;0;0;0;0;0;2106.4631377189044;3256.680682980992;6040.850074638076
ALEVIPR 0 2 22 87 399.24278899524 796.47102505686 796.48068829048 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 0.06758842550379995 0 0 404.22796346224 105699.21115950718 535482.9571224969 31861.157774525702 602034.402211528;33.26066936477699;0.07004231682060993 0.03262553971921278 5.9251385491228964E-05 0.003031633208957475 0.9297388842851689 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.23055482892653;404.7317573195174 0.7202677937323957;0.27973220626760437 0.7500448933950046;0.24995510660499548 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
ALEVIPR 1 2 22 88 404.22796346224 806.4413739908599 806.4510372244799 0.009663233620017309 NaN NaN NaN Cre01.g026550.t1.1 399.24278899524 9388.753377979152 48079.37442250919 3143.198614103804 53583.52224852161;33.2932949044962;0.06990153923375203 -0.03236152238286394 0 0 404.22796346224 105142.61299213648 535482.9571224969 14360.268949003324 604553.1666549129;33.260933382113336;0.06938320086311198 -0.08088338211333479 0 0 0.9302977722050324 PSM 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 156.73379516601562;4754.85009765625;628.1798095703125;1280.3272705078125;475.9390563964844;506.2529296875;228.01148986816406;330.1534729003906;438.1922302246094;488.2897033691406;516.9234008789062;398.7762451171875;262.80633544921875;434.8305358886719;2647.88525390625;1598.0269775390625;3349.700927734375;11815.7421875;32311.583984375;48688.15234375;53775.59765625;54288.8984375;40966.1796875;24644.236328125;15220.2626953125;5485.23486328125;2002.413818359375;1884.5279541015625 1560.5202558968292;5895.885203462351;1506.463482425685;1895.8590595661694;828.718062668089;596.2777112462152;55.28002041554802;0;0;0;0;0;0;0;372.99238888325226;0;549.2821034116009;8752.583658577718;28985.708798515407;45099.588752341544;49924.37766512193;50175.05555194293;36589.74641604704;20005.241673798955;10318.730326138559;321.1821120248933;0;0 404.2304659161266 1 1 32.552566666667;32.5894;32.626066666667;32.66255;32.698716666667;32.734883333333;32.77105;32.80755;32.843883333333;32.880366666667;32.916883333333;32.953366666667;32.990033333333;33.0267;33.063366666667;33.0997;33.136183333333;33.17285;33.20935;33.245683333333;33.282016666667;33.318516666667;33.355183333333;33.39185;33.428516666667;33.465333333333;33.502;33.538666666667 20690;19846.833984375;4301.30126953125;1802.526123046875;765.232421875;1132.2906494140625;1767.55078125;537.201416015625;1733.313232421875;5230.84716796875;22526.958984375;52285.56640625;87145.6796875;93966.2890625;98056.1484375;96633.4921875;149073.265625;298270.65625;516315.375;646046.125;622627.3125;471709.53125;305788.4375;172428.171875;92388.03125;48442.8984375;34055.1875;24209.21484375 26739.0766708578;23018.90809355345;4596.3714800765265;0;0;0;0;0;0;0;0;26688.034696038223;58671.67076850919;62616.07895798313;63830.068615044634;59531.92642822438;109096.64683204959;255419.46347195114;470590.1279760276;597447.3713889044;571155.6043507005;417365.39512916637;248572.3459342721;112340.52248271805;29429.13431258728;0;0;0
runs/run1/quant/minimal4_log.txt 0 → 100644
+ 46
− 0
View file @ f7642e81
2021-09-08 09:18:28.9000 minimal4 TRACE Input file: /YDHsjM/dataset/minimal4.mzlite
2021-09-08 09:18:28.9125 minimal4 TRACE Output directory: /YDHsjM/quant
2021-09-08 09:18:28.9177 minimal4 TRACE Parameters: { PerformLabeledQuantification = true
XicExtraction =
{ ScanTimeWindow = 2.0
MzWindow_Da = Fixed 0.7
XicProcessing =
Wavelet
{ Borderpadding = None
BorderPadMethod = Random
InternalPaddingMethod =
LinearInterpolation
HugeGapPaddingMethod = Zero
HugeGapPaddingDistance = 100.0
MinPeakDistance = None
MinPeakLength = Some 0.1
MaxPeakLength = 1.5
NoiseQuantile = 0.01
MinSNR = 0.01 }
TopKPSMs = None }
BaseLineCorrection = Some { MaxIterations = 10
Lambda = 6
P = 0.05 } }
2021-09-08 09:18:28.9177 minimal4 TRACE Now performing Quantification using: /YDHsjM/dataset/minimal4.mzlite and /YDHsjM/psmstats/minimal4.qpsm, Results will be written to: /YDHsjM/quant
2021-09-08 09:18:28.9177 minimal4 TRACE outFilePath:/YDHsjM/quant/minimal4.quant
2021-09-08 09:18:28.9331 minimal4 TRACE plotDirectory:/YDHsjM/quant/minimal4_plots
2021-09-08 09:18:28.9362 minimal4 TRACE Copy peptide DB into Memory
2021-09-08 09:18:28.9362 minimal4 TRACE Copy peptide DB into Memory: finished
2021-09-08 09:18:28.9362 minimal4 TRACE Get peptide lookUp function
2021-09-08 09:18:28.9480 minimal4 TRACE Get peptide lookUp function: finished
2021-09-08 09:18:28.9480 minimal4 TRACE Init connection to mass spectrum data.
2021-09-08 09:18:28.9694 minimal4 TRACE Create RetentionTime index
2021-09-08 09:18:28.9922 minimal4 TRACE Create RetentionTime index:finished
2021-09-08 09:18:28.9922 minimal4 TRACE Read and sort ms1s
2021-09-08 09:18:29.0115 minimal4 TRACE Read and sort ms1s:finished
2021-09-08 09:18:29.0159 minimal4 TRACE Read scored PSMs
2021-09-08 09:18:29.0159 minimal4 TRACE Read scored PSMs:finished
2021-09-08 09:18:29.0279 minimal4 TRACE Estimate precursor mz standard deviation and mz correction.
2021-09-08 09:18:29.0279 minimal4 TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
2021-09-08 09:18:29.0279 minimal4 TRACE init lookup functions
2021-09-08 09:18:29.0380 minimal4 TRACE init lookup functions:finished
2021-09-08 09:18:29.0380 minimal4 TRACE init quantification functions
2021-09-08 09:18:29.0380 minimal4 TRACE init quantification functions:finished
2021-09-08 09:18:29.0477 minimal4 TRACE executing quantification
2021-09-08 09:18:29.0477 minimal4 TRACE 0 peptides quantified
2021-09-08 09:18:29.1584 minimal4 TRACE executing quantification:finished
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