Skip to content
Snippets Groups Projects
Commit f7642e81 authored by Martin Kuhl's avatar Martin Kuhl
Browse files

adding ARC

parent 1e07bfe0
No related branches found
No related tags found
No related merge requests found
Showing
with 589 additions and 0 deletions
ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
2021-09-08 09:18:19.3537 PeptideSpectrumMatching TRACE CLIArguments: [InstrumentOutput ["/YDHsjM/dataset"];
PeptideDataBase
"/var/lib/cwl/stg0d5f9715-a95c-4464-aa32-6400aaa3657d/Minimal.db";
ParamFile
"/var/lib/cwl/stg913b968d-0ded-463e-8926-8591cbc8308b/peptideSpectrumMatchingParams.json";
OutputDirectory "psm"; Parallelism_Level 1]
2021-09-08 09:18:19.3876 PeptideSpectrumMatching TRACE Database found at given location (/var/lib/cwl/stg0d5f9715-a95c-4464-aa32-6400aaa3657d/Minimal.db)
2021-09-08 09:18:19.5828 PeptideSpectrumMatching TRACE Scoring multiple files: [|"/YDHsjM/dataset/minimal1.mzlite"; "/YDHsjM/dataset/minimal2.mzlite";
"/YDHsjM/dataset/minimal3.mzlite"; "/YDHsjM/dataset/minimal4.mzlite"|]
2021-09-08 09:18:19.5961 PeptideSpectrumMatching TRACE Program is running on 1 cores
PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext StringSequence
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 -1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 2.780764976 0.6779896705 0.0 26.3150871 0.7657267969 0.0 20.14279733 0.5594493789 0.0 ILVGDIK
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 8.635639049 0.0 0.6779896705 112.3264921 0.0 0.7657267969 45.72186797 0.0 0.5594493789 ILVGDIK
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 -1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 1.412423849 0.8192994029 0.0 0.0 1.0 0.0 7.323219744 0.7506817907 0.0 ALEVIPR
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 7.816376209 0.0 0.8192994029 74.99645487 0.0 1.0 29.37298389 0.0 0.7506817907 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 -1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 1.589227453 0.7970537368 0.0 11.5896755 0.8973792939 0.0 18.85459139 0.6070363597 0.0 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 7.830779576 0.0 0.7970537368 112.937008 0.0 0.8973792939 47.98049859 0.0 0.6070363597 ALEVIPR
PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext StringSequence
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 -1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 2.780764976 0.6779896705 0.0 26.3150871 0.7657267969 0.0 20.14279733 0.5594493789 0.0 ILVGDIK
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 8.635639049 0.0 0.6779896705 112.3264921 0.0 0.7657267969 45.72186797 0.0 0.5594493789 ILVGDIK
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 -1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 1.412423849 0.8192994029 0.0 0.0 1.0 0.0 7.323219744 0.7506817907 0.0 ALEVIPR
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 7.816376209 0.0 0.8192994029 74.99645487 0.0 1.0 29.37298389 0.0 0.7506817907 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 -1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 1.589227453 0.7970537368 0.0 11.5896755 0.8973792939 0.0 18.85459139 0.6070363597 0.0 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 7.830779576 0.0 0.7970537368 112.937008 0.0 0.8973792939 47.98049859 0.0 0.6070363597 ALEVIPR
2021-09-08 09:18:19.6118 minimal1 TRACE Input file: /YDHsjM/dataset/minimal1.mzlite
2021-09-08 09:18:19.6258 minimal1 TRACE Output directory: /YDHsjM/psm
2021-09-08 09:18:19.6386 minimal1 TRACE Parameters: { ChargeStateDeterminationParams = { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
LookUpPPM = 30.0
nTerminalSeries = <fun:toDomain@147-6>
cTerminalSeries = <fun:toDomain@167-13>
AndromedaParams = { PMinPMax = (4, 10)
MatchingIonTolerancePPM = 100.0 } }
2021-09-08 09:18:19.6386 minimal1 TRACE Result file path: /YDHsjM/psm/minimal1.psm
2021-09-08 09:18:19.6487 minimal1 TRACE Copy peptide DB into Memory.
2021-09-08 09:18:19.6737 minimal1 TRACE Copy peptide DB into Memory: finished.
2021-09-08 09:18:19.6778 minimal1 TRACE Prepare processing functions.
2021-09-08 09:18:19.6778 minimal1 TRACE Charge parameters: { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
2021-09-08 09:18:19.7560 minimal1 TRACE DB parameters: { Name = "Minimal"
DbFolder = "/YDHsjM/db"
FastaPath =
"/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta"
FastaHeaderToName = <fun:getSDBParams@907>
Protease = { Name = "Trypsin"
Expression = <fun:Trypsin@175> }
MinMissedCleavages = 0
MaxMissedCleavages = 2
MaxMass = 15000.0
MinPepLength = 4
MaxPepLength = 65
IsotopicMod = [{ Name = "N15"
SourceEl = Di { Symbol = "N"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 }
TargetEl = Di { Symbol = "N15"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 } }]
MassMode = Monoisotopic
MassFunction = <fun:memoizeP@25>
FixedMods = []
VariableMods = [{ Name = "Acetyl(Protein N-Term)"
Accession = "1"
Description = "Acetylation of the protein N-terminus"
IsBiological = true
Composition = "C2H2O"
Site = [Any ProteinNterm]
MType = Plus
XModCode = "ac" }; { Name = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" }]
VarModThreshold = 4 }
2021-09-08 09:18:19.7664 minimal1 TRACE Finished preparing processing functions.
2021-09-08 09:18:19.7664 minimal1 TRACE Init connection to input data base.
2021-09-08 09:18:19.8007 minimal1 TRACE Run ID: sample=0
2021-09-08 09:18:19.8007 minimal1 TRACE Starting charge state determination.
2021-09-08 09:18:20.0143 minimal1 TRACE Finished charge state determination.
2021-09-08 09:18:20.0259 minimal1 TRACE ProteomIQon.PeptideSpectrumMatching+scoreSpectra@372
2021-09-08 09:18:20.0374 minimal1 TRACE Starting peptide spectrum matching.
2021-09-08 09:18:20.0527 minimal1 TRACE 3 spectra with charge 2
2021-09-08 09:18:20.0580 minimal1 TRACE 2 spectra with charge 3
2021-09-08 09:18:20.0580 minimal1 TRACE 3 spectra with charge 2 processed
2021-09-08 09:18:20.0686 minimal1 TRACE 0
2021-09-08 09:18:20.1729 minimal1 TRACE 2 spectra with charge 3 processed
2021-09-08 09:18:20.1803 minimal1 TRACE 0
2021-09-08 09:18:20.1937 minimal1 TRACE Finished peptide spectrum matching.
2021-09-08 09:18:20.2025 minimal1 TRACE Done.
PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext StringSequence
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 -1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 2.780764976 0.6779896705 0.0 26.3150871 0.7657267969 0.0 20.14279733 0.5594493789 0.0 ILVGDIK
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 8.635639049 0.0 0.6779896705 112.3264921 0.0 0.7657267969 45.72186797 0.0 0.5594493789 ILVGDIK
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 -1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 1.412423849 0.8192994029 0.0 0.0 1.0 0.0 7.323219744 0.7506817907 0.0 ALEVIPR
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 7.816376209 0.0 0.8192994029 74.99645487 0.0 1.0 29.37298389 0.0 0.7506817907 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 -1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 1.589227453 0.7970537368 0.0 11.5896755 0.8973792939 0.0 18.85459139 0.6070363597 0.0 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 7.830779576 0.0 0.7970537368 112.937008 0.0 0.8973792939 47.98049859 0.0 0.6070363597 ALEVIPR
2021-09-08 09:18:20.2065 minimal2 TRACE Input file: /YDHsjM/dataset/minimal2.mzlite
2021-09-08 09:18:20.2065 minimal2 TRACE Output directory: /YDHsjM/psm
2021-09-08 09:18:20.2181 minimal2 TRACE Parameters: { ChargeStateDeterminationParams = { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
LookUpPPM = 30.0
nTerminalSeries = <fun:toDomain@147-6>
cTerminalSeries = <fun:toDomain@167-13>
AndromedaParams = { PMinPMax = (4, 10)
MatchingIonTolerancePPM = 100.0 } }
2021-09-08 09:18:20.2181 minimal2 TRACE Result file path: /YDHsjM/psm/minimal2.psm
2021-09-08 09:18:20.2181 minimal2 TRACE Copy peptide DB into Memory.
2021-09-08 09:18:20.2290 minimal2 TRACE Copy peptide DB into Memory: finished.
2021-09-08 09:18:20.2290 minimal2 TRACE Prepare processing functions.
2021-09-08 09:18:20.2357 minimal2 TRACE Charge parameters: { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
2021-09-08 09:18:20.2357 minimal2 TRACE DB parameters: { Name = "Minimal"
DbFolder = "/YDHsjM/db"
FastaPath =
"/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta"
FastaHeaderToName = <fun:getSDBParams@907>
Protease = { Name = "Trypsin"
Expression = <fun:Trypsin@175> }
MinMissedCleavages = 0
MaxMissedCleavages = 2
MaxMass = 15000.0
MinPepLength = 4
MaxPepLength = 65
IsotopicMod = [{ Name = "N15"
SourceEl = Di { Symbol = "N"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 }
TargetEl = Di { Symbol = "N15"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 } }]
MassMode = Monoisotopic
MassFunction = <fun:memoizeP@25>
FixedMods = []
VariableMods = [{ Name = "Acetyl(Protein N-Term)"
Accession = "1"
Description = "Acetylation of the protein N-terminus"
IsBiological = true
Composition = "C2H2O"
Site = [Any ProteinNterm]
MType = Plus
XModCode = "ac" }; { Name = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" }]
VarModThreshold = 4 }
2021-09-08 09:18:20.2357 minimal2 TRACE Finished preparing processing functions.
2021-09-08 09:18:20.2480 minimal2 TRACE Init connection to input data base.
2021-09-08 09:18:20.2646 minimal2 TRACE Run ID: sample=0
2021-09-08 09:18:20.2685 minimal2 TRACE Starting charge state determination.
2021-09-08 09:18:20.3256 minimal2 TRACE Finished charge state determination.
2021-09-08 09:18:20.3361 minimal2 TRACE ProteomIQon.PeptideSpectrumMatching+scoreSpectra@372
2021-09-08 09:18:20.3361 minimal2 TRACE Starting peptide spectrum matching.
2021-09-08 09:18:20.3361 minimal2 TRACE 3 spectra with charge 2
2021-09-08 09:18:20.3477 minimal2 TRACE 2 spectra with charge 3
2021-09-08 09:18:20.3477 minimal2 TRACE 3 spectra with charge 2 processed
2021-09-08 09:18:20.3477 minimal2 TRACE 0
2021-09-08 09:18:20.3722 minimal2 TRACE 2 spectra with charge 3 processed
2021-09-08 09:18:20.3807 minimal2 TRACE 0
2021-09-08 09:18:20.3913 minimal2 TRACE Finished peptide spectrum matching.
2021-09-08 09:18:20.3913 minimal2 TRACE Done.
PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext StringSequence
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 -1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 2.780764976 0.6779896705 0.0 26.3150871 0.7657267969 0.0 20.14279733 0.5594493789 0.0 ILVGDIK
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 8.635639049 0.0 0.6779896705 112.3264921 0.0 0.7657267969 45.72186797 0.0 0.5594493789 ILVGDIK
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 -1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 1.412423849 0.8192994029 0.0 0.0 1.0 0.0 7.323219744 0.7506817907 0.0 ALEVIPR
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 7.816376209 0.0 0.8192994029 74.99645487 0.0 1.0 29.37298389 0.0 0.7506817907 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 -1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 1.589227453 0.7970537368 0.0 11.5896755 0.8973792939 0.0 18.85459139 0.6070363597 0.0 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 7.830779576 0.0 0.7970537368 112.937008 0.0 0.8973792939 47.98049859 0.0 0.6070363597 ALEVIPR
2021-09-08 09:18:20.3992 minimal3 TRACE Input file: /YDHsjM/dataset/minimal3.mzlite
2021-09-08 09:18:20.4076 minimal3 TRACE Output directory: /YDHsjM/psm
2021-09-08 09:18:20.4076 minimal3 TRACE Parameters: { ChargeStateDeterminationParams = { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
LookUpPPM = 30.0
nTerminalSeries = <fun:toDomain@147-6>
cTerminalSeries = <fun:toDomain@167-13>
AndromedaParams = { PMinPMax = (4, 10)
MatchingIonTolerancePPM = 100.0 } }
2021-09-08 09:18:20.4076 minimal3 TRACE Result file path: /YDHsjM/psm/minimal3.psm
2021-09-08 09:18:20.4191 minimal3 TRACE Copy peptide DB into Memory.
2021-09-08 09:18:20.4191 minimal3 TRACE Copy peptide DB into Memory: finished.
2021-09-08 09:18:20.4273 minimal3 TRACE Prepare processing functions.
2021-09-08 09:18:20.4273 minimal3 TRACE Charge parameters: { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
2021-09-08 09:18:20.4385 minimal3 TRACE DB parameters: { Name = "Minimal"
DbFolder = "/YDHsjM/db"
FastaPath =
"/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta"
FastaHeaderToName = <fun:getSDBParams@907>
Protease = { Name = "Trypsin"
Expression = <fun:Trypsin@175> }
MinMissedCleavages = 0
MaxMissedCleavages = 2
MaxMass = 15000.0
MinPepLength = 4
MaxPepLength = 65
IsotopicMod = [{ Name = "N15"
SourceEl = Di { Symbol = "N"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 }
TargetEl = Di { Symbol = "N15"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 } }]
MassMode = Monoisotopic
MassFunction = <fun:memoizeP@25>
FixedMods = []
VariableMods = [{ Name = "Acetyl(Protein N-Term)"
Accession = "1"
Description = "Acetylation of the protein N-terminus"
IsBiological = true
Composition = "C2H2O"
Site = [Any ProteinNterm]
MType = Plus
XModCode = "ac" }; { Name = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" }]
VarModThreshold = 4 }
2021-09-08 09:18:20.4385 minimal3 TRACE Finished preparing processing functions.
2021-09-08 09:18:20.4459 minimal3 TRACE Init connection to input data base.
2021-09-08 09:18:20.4645 minimal3 TRACE Run ID: sample=0
2021-09-08 09:18:20.4698 minimal3 TRACE Starting charge state determination.
2021-09-08 09:18:20.5163 minimal3 TRACE Finished charge state determination.
2021-09-08 09:18:20.5271 minimal3 TRACE ProteomIQon.PeptideSpectrumMatching+scoreSpectra@372
2021-09-08 09:18:20.5271 minimal3 TRACE Starting peptide spectrum matching.
2021-09-08 09:18:20.5365 minimal3 TRACE 3 spectra with charge 2
2021-09-08 09:18:20.5365 minimal3 TRACE 2 spectra with charge 3
2021-09-08 09:18:20.5365 minimal3 TRACE 3 spectra with charge 2 processed
2021-09-08 09:18:20.5365 minimal3 TRACE 0
2021-09-08 09:18:20.5559 minimal3 TRACE 2 spectra with charge 3 processed
2021-09-08 09:18:20.5559 minimal3 TRACE 0
2021-09-08 09:18:20.5672 minimal3 TRACE Finished peptide spectrum matching.
2021-09-08 09:18:20.5672 minimal3 TRACE Done.
PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext StringSequence
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 -1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 2.780764976 0.6779896705 0.0 26.3150871 0.7657267969 0.0 20.14279733 0.5594493789 0.0 ILVGDIK
sample=1-period=1-cycle=2033-experiment=4_0_2_0 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 -1 8.635639049 0.0 0.6779896705 112.3264921 0.0 0.7657267969 45.72186797 0.0 0.5594493789 ILVGDIK
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 -1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 1.412423849 0.8192994029 0.0 0.0 1.0 0.0 7.323219744 0.7506817907 0.0 ALEVIPR
sample=1-period=1-cycle=2043-experiment=5_2_2_0 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 -1 7.816376209 0.0 0.8192994029 74.99645487 0.0 1.0 29.37298389 0.0 0.7506817907 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 -1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 1.589227453 0.7970537368 0.0 11.5896755 0.8973792939 0.0 18.85459139 0.6070363597 0.0 ALEVIPR
sample=1-period=1-cycle=2038-experiment=7_1_2_0 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 -1 7.830779576 0.0 0.7970537368 112.937008 0.0 0.8973792939 47.98049859 0.0 0.6070363597 ALEVIPR
2021-09-08 09:18:20.5672 minimal4 TRACE Input file: /YDHsjM/dataset/minimal4.mzlite
2021-09-08 09:18:20.5817 minimal4 TRACE Output directory: /YDHsjM/psm
2021-09-08 09:18:20.5817 minimal4 TRACE Parameters: { ChargeStateDeterminationParams = { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
LookUpPPM = 30.0
nTerminalSeries = <fun:toDomain@147-6>
cTerminalSeries = <fun:toDomain@167-13>
AndromedaParams = { PMinPMax = (4, 10)
MatchingIonTolerancePPM = 100.0 } }
2021-09-08 09:18:20.5890 minimal4 TRACE Result file path: /YDHsjM/psm/minimal4.psm
2021-09-08 09:18:20.5890 minimal4 TRACE Copy peptide DB into Memory.
2021-09-08 09:18:20.5973 minimal4 TRACE Copy peptide DB into Memory: finished.
2021-09-08 09:18:20.5973 minimal4 TRACE Prepare processing functions.
2021-09-08 09:18:20.5973 minimal4 TRACE Charge parameters: { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
2021-09-08 09:18:20.6100 minimal4 TRACE DB parameters: { Name = "Minimal"
DbFolder = "/YDHsjM/db"
FastaPath =
"/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta"
FastaHeaderToName = <fun:getSDBParams@907>
Protease = { Name = "Trypsin"
Expression = <fun:Trypsin@175> }
MinMissedCleavages = 0
MaxMissedCleavages = 2
MaxMass = 15000.0
MinPepLength = 4
MaxPepLength = 65
IsotopicMod = [{ Name = "N15"
SourceEl = Di { Symbol = "N"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 }
TargetEl = Di { Symbol = "N15"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 } }]
MassMode = Monoisotopic
MassFunction = <fun:memoizeP@25>
FixedMods = []
VariableMods = [{ Name = "Acetyl(Protein N-Term)"
Accession = "1"
Description = "Acetylation of the protein N-terminus"
IsBiological = true
Composition = "C2H2O"
Site = [Any ProteinNterm]
MType = Plus
XModCode = "ac" }; { Name = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" }]
VarModThreshold = 4 }
2021-09-08 09:18:20.6100 minimal4 TRACE Finished preparing processing functions.
2021-09-08 09:18:20.6265 minimal4 TRACE Init connection to input data base.
2021-09-08 09:18:20.6439 minimal4 TRACE Run ID: sample=0
2021-09-08 09:18:20.6476 minimal4 TRACE Starting charge state determination.
2021-09-08 09:18:20.6912 minimal4 TRACE Finished charge state determination.
2021-09-08 09:18:20.7001 minimal4 TRACE ProteomIQon.PeptideSpectrumMatching+scoreSpectra@372
2021-09-08 09:18:20.7001 minimal4 TRACE Starting peptide spectrum matching.
2021-09-08 09:18:20.7090 minimal4 TRACE 3 spectra with charge 2
2021-09-08 09:18:20.7090 minimal4 TRACE 2 spectra with charge 3
2021-09-08 09:18:20.7090 minimal4 TRACE 3 spectra with charge 2 processed
2021-09-08 09:18:20.7161 minimal4 TRACE 0
2021-09-08 09:18:20.7284 minimal4 TRACE 2 spectra with charge 3 processed
2021-09-08 09:18:20.7284 minimal4 TRACE 0
2021-09-08 09:18:20.7394 minimal4 TRACE Finished peptide spectrum matching.
2021-09-08 09:18:20.7394 minimal4 TRACE Done.
2021-09-07 09:57:25.9761 minimal TRACE Input file: /FuNLno/mzlite/minimal.mzlite
2021-09-07 09:57:25.9907 minimal TRACE Output directory: /FuNLno/psm
2021-09-07 09:57:26.0038 minimal TRACE Parameters: { ChargeStateDeterminationParams = { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
LookUpPPM = 30.0
nTerminalSeries = <fun:toDomain@147-6>
cTerminalSeries = <fun:toDomain@167-13>
AndromedaParams = { PMinPMax = (4, 10)
MatchingIonTolerancePPM = 100.0 } }
2021-09-07 09:57:26.0079 minimal TRACE Result file path: /FuNLno/psm/minimal.psm
2021-09-07 09:57:26.0079 minimal TRACE Copy peptide DB into Memory.
2021-09-07 09:57:26.0343 minimal TRACE Copy peptide DB into Memory: finished.
2021-09-07 09:57:26.0389 minimal TRACE Prepare processing functions.
2021-09-07 09:57:26.0389 minimal TRACE Charge parameters: { ExpectedMinimalCharge = 2
ExpectedMaximumCharge = 5
Width = 1.1
MinIntensity = 0.15
DeltaMinIntensity = 0.3
NrOfRndSpectra = 10000 }
2021-09-07 09:57:26.1145 minimal TRACE DB parameters: { Name = "Minimal"
DbFolder = "C:\Users\d_zimmer\ProteomIQonErrorTesting\MinimalData\0_peptideDB"
FastaPath =
"C:\Users\d_zimmer\ProteomIQonErrorTesting\MinimalData\0_peptideDB\example.fasta"
FastaHeaderToName = <fun:getSDBParams@907>
Protease = { Name = "Trypsin"
Expression = <fun:Trypsin@175> }
MinMissedCleavages = 0
MaxMissedCleavages = 2
MaxMass = 15000.0
MinPepLength = 4
MaxPepLength = 65
IsotopicMod = [{ Name = "N15"
SourceEl = Di { Symbol = "N"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 }
TargetEl = Di { Symbol = "N15"
X = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 15
Mass = 15.0001089
NatAbundance = 0.00364
RelAtomicMass = 14.0067 }
Xcomp = 0.99636
X1 = { AtomicSymbol = "N"
AtomicNumberZ = 7
MassNumber = 14
Mass = 14.003074
NatAbundance = 0.99636
RelAtomicMass = 14.0067 }
X1comp = 0.00364
Root = -273.7252747 } }]
MassMode = Monoisotopic
MassFunction = <fun:memoizeP@25>
FixedMods = []
VariableMods = [{ Name = "Acetyl(Protein N-Term)"
Accession = "1"
Description = "Acetylation of the protein N-terminus"
IsBiological = true
Composition = "C2H2O"
Site = [Any ProteinNterm]
MType = Plus
XModCode = "ac" }; { Name = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" }]
VarModThreshold = 4 }
2021-09-07 09:57:26.1243 minimal TRACE Finished preparing processing functions.
2021-09-07 09:57:26.1319 minimal TRACE Init connection to input data base.
2021-09-07 09:57:26.1611 minimal TRACE Run ID: sample=0
2021-09-07 09:57:26.1661 minimal TRACE Starting charge state determination.
2021-09-07 09:57:26.3510 minimal TRACE Finished charge state determination.
2021-09-07 09:57:26.3628 minimal TRACE ProteomIQon.PeptideSpectrumMatching+scoreSpectra@372
2021-09-07 09:57:26.3765 minimal TRACE Starting peptide spectrum matching.
2021-09-07 09:57:26.3937 minimal TRACE 3 spectra with charge 2
2021-09-07 09:57:26.3998 minimal TRACE 2 spectra with charge 3
2021-09-07 09:57:26.4056 minimal TRACE 3 spectra with charge 2 processed
2021-09-07 09:57:26.4056 minimal TRACE 0
2021-09-07 09:57:26.5217 minimal TRACE 2 spectra with charge 3 processed
2021-09-07 09:57:26.5292 minimal TRACE 0
2021-09-07 09:57:26.5454 minimal TRACE Finished peptide spectrum matching.
2021-09-07 09:57:26.5575 minimal TRACE Done.
{"ChargeStateDeterminationParams":{"ExpectedMinimalCharge":2,"ExpectedMaximumCharge":5,"Width":1.1,"MinIntensity":0.15,"DeltaMinIntensity":0.3,"NrOfRndSpectra":10000},"LookUpPPM":30.0,"nTerminalSeries":{"Case":"B"},"cTerminalSeries":{"Case":"Y"},"Andromeda":{"PMinPMax":{"Item1":4,"Item2":10},"MatchingIonTolerancePPM":100.0}}
2021-09-08 09:18:22.3847 PSMStatistics TRACE CLIArguments: [PSMs ["/YDHsjM/psm"];
PeptideDataBase
"/var/lib/cwl/stg4a5f61b2-3355-48cd-bf1a-bb05bc4f8062/Minimal.db";
ParamFile
"/var/lib/cwl/stg30675f59-9187-4f70-98fa-cffe79774679/pSMStatisticsParamsFixed.json";
OutputDirectory "psmstats"; Parallelism_Level 1]
2021-09-08 09:18:22.5312 PSMStatistics TRACE Database found at given location (/var/lib/cwl/stg4a5f61b2-3355-48cd-bf1a-bb05bc4f8062/Minimal.db)
2021-09-08 09:18:22.6172 PSMStatistics TRACE Processing multiple files: [|"/YDHsjM/psm/minimal1.psm"; "/YDHsjM/psm/minimal2.psm";
"/YDHsjM/psm/minimal3.psm"; "/YDHsjM/psm/minimal4.psm"|]
2021-09-08 09:18:22.6307 PSMStatistics TRACE Program is running on 1 cores
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
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
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment