diogobor
commented
5 months ago Dear Jiale Zhao,
This error happened because the current version of Scout requires a processor with at least 4 cores to run the search. If you are using a Virtual Machine or a processor that contains less than 4 cores, Scout shows the error you pointed out.
We're optimizing the algorithm to be compatible with processors that contain less then 4 cores.
Best, Diogo
Heisenburger2020
Dear Sir/Madam,
I am Jiale Zhao, a Ph.D. student at the Institute of Computation in China.
I have met an error when running scout on Juri's(2021) dataset(DSSO). Would you be so kind to tell me how to solve this?
The error and parameter are as follows:
{ "BDP_Mode": false, "MSFileExtension": ".mgf", "PPMMS1Tolerance": 3.0, "PPMMS2Tolerance": 5.0, "PerformShotgunSearch": false, "PerformCleaveXLSearch": true, "SaveSpectraToResults": false, "MaxQueryResults": 4, "MinPepLength": 6, "MaxPepLength": 60, "MinPepMass": 600.0, "MaxPepMass": 6000.0, "FastaFile": "C:\Users\10076\Desktop\scout\uniprot-k12-filtered-proteome_UP000000625.fasta", "RawPath": null, "AddMinusOneIsotope": false, "CarbonIsotopeShift": 1.0033548, "IsotopicPossibilitiesPrecursor": 1, "MiscleavageNum": 2, "Enzyme": { "Name": "Trypsin", "CTerminus": true, "Sites": "KR", "BlockedBy": "P" }, "EnzymeSpecificity": 0, "MaximumVariableModsPerPeptide": 3, "StaticModifications": [ { "MassShift": 57.02146, "Name": "Carbamidomethyl", "IsCTerm": false, "IsNTerm": false, "IsVariable": false, "TargetResidues": "C", "ModIndex": 1 } ], "VariableModifications": [ { "MassShift": 15.9949, "Name": "Oxidation of Methionine", "IsCTerm": false, "IsNTerm": false, "IsVariable": true, "TargetResidues": "M", "ModIndex": 2 } ], "ExtraAminoacids": null, "SearchLoopLinks": true, "IonPairMaxCharge": 2, "CXLReagent": { "Name": "DSSO", "LightTag": "Light", "LightFragment": 54.01056468, "HeavyTag": "Heavy", "HeavyFragment": 85.98263585, "WholeTag": "Full", "WholeMass": 158.00376533, "DeltaShift": 31.972071169999992, "Targets": "K", "TargetNTerm": true }, "FullPairsOnly": false, "PairFinderPPM": 5.0, "MinBinMZ": 200.0, "MaxBinMZ": 1800.0, "BinSize": 0.02, "Offset": 0.0, "ScoreFunction": 1, "MS2NormalizationTypes": 2, "NormalizationWindowWidth": 80.0, "NormalizationWindowPeaksKept": 13, "AddPrecursorToDotProduct": false, "AddIonPairsToDotProduct": false, "ApplyMZRangeWeighting": false, "ReorderCleaveCandidateScores": true, "RemoveIonPairsFromExperimentalMS": true, "RemovePrecursorFromExperimentalMS": true, "ReorderingMethod": 0, "ReorderingCombinatorialDepthHeavy": 3, "ReorderingCombinatorialDepthLight": 2, "FastaBatchSize": 30000, "ParallelPSMs": true, "QueryBatches": null, "MergeDatabase": false, "MethionineInitiator": true, "AddDecoys": true, "AddContaminants": true, "DontShowContaminants": true, "DecoyTag": "Reverse", "DecoyGenerationMode": 0, "AddUnlabelledDecoys": false, "UnlabelledDecoyTag": "Unlabelled", "OffsetUnlabelledDecoy": true, "OffsetUnlabelled": 2, "UnlabelledDecoysGenerationMode": 4, "AddLocusStringToPeptides": true, "DeconvolutionForPairSearching": true, "DeconvolutionForMSScoring": false, "SilacSearch": false, "SilacHybridMode": false, "SilacGroups": [ { "GroupName": "Heavy", "GroupAminoacids": [ { "TargetResidue": "K", "MassShift": 8.0141988131999 }, { "TargetResidue": "R", "MassShift": 10.0082685996 } ] }, { "GroupName": "Light", "GroupAminoacids": [ { "TargetResidue": "K", "MassShift": 0.0 }, { "TargetResidue": "R", "MassShift": 0.0 } ] } ], "SilacSearchNormalPeptides": false, "IsobaricLabelling_Search": false, "IsobaricLabelling_Mods": [ { "MassShift": 144.1, "Name": "iTRAQ - 4", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 7 }, { "MassShift": 304.2022, "Name": "iTRAQ - 8", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 6 }, { "MassShift": 229.1629321141, "Name": "TMT - 6plex", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 8 }, { "MassShift": 229.1629321141, "Name": "TMT - 10plex", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 9 }, { "MassShift": 229.1629321141, "Name": "TMT - 11plex", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 10 }, { "MassShift": 304.207146, "Name": "TMT - 16plex (TMTpro)", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 11 }, { "MassShift": 304.207146, "Name": "TMT - 18plex (TMTpro)", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 12 } ], "SelectedIsobaricLabelling_Mod": { "MassShift": 304.207146, "Name": "TMT - 16plex (TMTpro)", "IsCTerm": false, "IsNTerm": true, "IsVariable": false, "TargetResidues": "K", "ModIndex": 11 }, "IsobaricLabelling_AllowedFreeResidues": 0, "CalculatePairIntensities": true, "AddXLasVariableMod": false, "IsotopesInTheoreticalMS": 2, "MaxChargeInTheoreticalMS": 2, "BonusMode": true, "BonusScore": 0.001, "ApplyNeutralLossH2O": false, "ApplyNeutralLossNH3": false, "StarIntensity": 0.7, "FastaDistinctByLocus": true, "ApplyQuantileIntensityThreshold": false, "QuantileIntensityThreshold": 0.3 }