Commit b501cf0f authored by Martin Kuhl's avatar Martin Kuhl
Browse files

Add Sample ARC

parent 2b411e8a
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>Cre02.g143307.t1.1 ClpC chaperone, Hsp100 family ALS=CLPC1 DBV=JGI5.5 GN=CLPC1 OS=Chlamydomonas reinhardtii SV=1 TOU=Cre
MRLIEDCLAERILVGDIKEGDVVIMDVDPDGSIAVLAGDKKMRAEIDAVPAGIA*
>Cre01.g026550.t1.1 T-complex protein 1, eta subunit ALS=CCT7 DBV=JGI5.5 GN=CCT7 OS=Chlamydomonas reinhardtii SV=1 TOU=Cre
MMPMMGMQPQIILLKEGTDTSQGKAQLISNINACMAVVDTVRTTLGPRGMDKLIHDARGVTISNDGATIMKLLDIVHPAA
KSLVDVSLAQDAEVGDGTTSVVVLAGEFLKEAKPFIEEGVHPRSLMKSFRQASVLAVERLKALAISLEDKHMEEKKDLLK
KCAMTTLNSKLVSGEKEFFAQMVVDAVSTLDPSTLDLKMVGIKKVQGGGLRDSFLVDGVAFKKTFSYAGFEQQPKSFHNP
KILVLNIELELKAEKENAEIRLDDPAKYQSIVDAEWNIIYDKLAKCVASGANIVLSRLAIGDLATQYFADRNIFCAGRVE
TGDMERVTKATGAKVQTTVNNLDTKVLGTCERFEERQVGAERYNLFTGCPAARTATLVLRGGSEQFIDEADRSLHDAIMI
VRRALKHAQIVPGGGAIEMELSKYLSEHSLQYTSKAQLFIRAFAKALEVIPRQLCNNAGFDATDVLNQLRHKHALADGSG
RCYGMDVNTGGVCDTYDAFVWEPALVKINAIQAATEAACLILSVDETVRNPKSEVPDAASGAAAQAAMGGRGRGRGGGGM
RGRGMRR*
2021-09-08 09:18:17.2387 PeptideDB_Minimal TRACE Initializing PeptideDB at: /YDHsjM/db
2021-09-08 09:18:17.2689 PeptideDB_Minimal TRACE searchDBParams: { Name = "Minimal"
DbFolder = "/YDHsjM/db"
FastaPath =
"/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta"
FastaHeaderToName = <fun:parseProteinIdUsing@179-1>
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 = "Oxidation'Met'"
Accession = "35"
Description = "Oxidation"
IsBiological = true
Composition = "O"
Site = [Specific (Met, Residual)]
MType = Plus
XModCode = "ox" };
{ 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" }]
VarModThreshold = 4 }
2021-09-08 09:18:17.7127 PeptideDB_Minimal TRACE Successfully created PeptideDB
2021-09-08 09:18:17.7127 PeptideDB_Minimal TRACE Set Index on data base if not present.
2021-09-08 09:18:17.7365 PeptideDB_Minimal TRACE Set Index on data base if not present: finished
2021-09-08 09:18:17.7365 PeptideDB_Minimal TRACE Done
2021-09-08 09:18:17.0584 PeptideDB TRACE CLIArguments [FastaPath "/var/lib/cwl/stg56841850-2554-4dc4-86ee-a56610fc9a5b/example.fasta";
ParamFile
"/var/lib/cwl/stgdafdc63f-52fd-45e0-822d-dd7533f817ed/peptideDBParams.json";
OutputDirectory "db"]
{"Name":"Minimal","ParseProteinIDRegexPattern":"Cre\\S+|QProt_\\S+","Protease":{"Case":"Trypsin"},"MinMissedCleavages":0,"MaxMissedCleavages":2,"MaxMass":15000.0,"MinPepLength":4,"MaxPepLength":65,"IsotopicMod":[{"Case":"N15"}],"MassMode":{"Case":"Monoisotopic"},"FixedMods":[],"VariableMods":[{"Case":"Oxidation'Met'"},{"Case":"Acetylation'ProtNTerm'"}],"VarModThreshold":4}
\ No newline at end of file
{
"Compress": 0,
"StartRetentionTime": null,
"EndRetentionTime": null,
"MS1PeakPicking": {
"Case": "ProfilePeaks"
},
"MS2PeakPicking": {
"Case": "ProfilePeaks"
}
}
\ No newline at end of file
{
"ProteinIdentifierRegex": "id",
"Protein": {
"Case": "Maximal"
},
"Peptide": {
"Case": "Minimal"
},
"GroupFiles": true,
"GetQValue": {
"Case": "Storey"
}
}
\ No newline at end of file
2021-09-08 09:18:25.0318 ProteinInference_createClassItemCollection TRACE Reading GFF3 file
2021-09-08 09:18:25.0696 ProteinInference_createClassItemCollection TRACE Assigning FastA sequences to protein model info
2021-09-08 09:18:25.0792 ProteinInference_createClassItemCollection TRACE Build classification map
2021-09-08 09:18:24.9088 ProteinInference_inferProteins TRACE InputFilePath = [|"/YDHsjM/psmstats/minimal1.qpsm"; "/YDHsjM/psmstats/minimal2.qpsm";
"/YDHsjM/psmstats/minimal3.qpsm"; "/YDHsjM/psmstats/minimal4.qpsm"|]
2021-09-08 09:18:24.9200 ProteinInference_inferProteins TRACE InputGFF3Path = None
2021-09-08 09:18:24.9200 ProteinInference_inferProteins TRACE OutputFilePath = /YDHsjM/prot
2021-09-08 09:18:24.9330 ProteinInference_inferProteins TRACE Protein inference parameters = { TryGetProteinIdentifier = <fun:tryParseProteinIdUsing@184>
Protein = Maximal
Peptide = Minimal
GroupFiles = true
GetQValue = Storey }
2021-09-08 09:18:24.9371 ProteinInference_inferProteins TRACE Copy peptide DB into Memory.
2021-09-08 09:18:24.9513 ProteinInference_inferProteins TRACE Copy peptide DB into Memory: finished.
2021-09-08 09:18:24.9513 ProteinInference_inferProteins TRACE Start building ClassItemCollection
2021-09-08 09:18:25.1091 ProteinInference_inferProteins TRACE Classify and Infer Proteins
2021-09-08 09:18:24.6709 ProteinInference TRACE CLIArguments: [InputFolder ["/YDHsjM/psmstats"];
PeptideDataBase
"/var/lib/cwl/stgdddd854e-69da-4075-a168-721c25f724a9/Minimal.db";
ParamFile
"/var/lib/cwl/stg0b674556-1709-4d2c-9a18-3521efd66a63/ProteinInferenceParams.json";
OutputDirectory "prot"]
2021-09-08 09:18:24.7087 ProteinInference TRACE Database found at given location (/var/lib/cwl/stgdddd854e-69da-4075-a168-721c25f724a9/Minimal.db)
2021-09-08 09:18:24.8982 ProteinInference TRACE Inputfiles: [|"/YDHsjM/psmstats/minimal1.qpsm"; "/YDHsjM/psmstats/minimal2.qpsm";
"/YDHsjM/psmstats/minimal3.qpsm"; "/YDHsjM/psmstats/minimal4.qpsm"|]
2021-09-08 09:18:25.1861 ProteinInference_readAndInferFile TRACE Getting proteins with peptide sequence from db
2021-09-08 09:18:25.2027 ProteinInference_readAndInferFile TRACE Perfom digestion on reversed proteins for decoy set
2021-09-08 09:18:25.2199 ProteinInference_readAndInferFile TRACE Map peptide sequences to proteins
2021-09-08 09:18:25.2363 ProteinInference_readAndInferFile TRACE Create combined list
2021-09-08 09:18:25.2574 ProteinInference_readAndInferFile TRACE Create a map with peptide scores
2021-09-08 09:18:25.2688 ProteinInference_readAndInferFile TRACE Assign scores to decoy set
2021-09-08 09:18:25.2768 ProteinInference_readAndInferFile TRACE Assign target and decoy scores inferred proteins
2021-09-08 09:18:25.2960 ProteinInference_readAndInferFile TRACE Calculate q values for all proteins
2021-09-08 09:18:25.4499 ProteinInference_readAndInferFile TRACE Writing now minimal1
2021-09-08 09:18:25.4755 ProteinInference_readAndInferFile TRACE File written to /YDHsjM/prot/minimal1.prot
2021-09-08 09:18:25.4837 ProteinInference_readAndInferFile TRACE Writing now minimal2
2021-09-08 09:18:25.4931 ProteinInference_readAndInferFile TRACE File written to /YDHsjM/prot/minimal2.prot
2021-09-08 09:18:25.4962 ProteinInference_readAndInferFile TRACE Writing now minimal3
2021-09-08 09:18:25.4962 ProteinInference_readAndInferFile TRACE File written to /YDHsjM/prot/minimal3.prot
2021-09-08 09:18:25.5069 ProteinInference_readAndInferFile TRACE Writing now minimal4
2021-09-08 09:18:25.5069 ProteinInference_readAndInferFile TRACE File written to /YDHsjM/prot/minimal4.prot
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