Add Sample ARC

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externals/example.fasta

+>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*

runs/run1/db/PeptideDB_Minimal_log.txt

+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 

runs/run1/db/PeptideDB_log.txt

+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"] 

runs/run1/db/peptideDBParams.json

+{"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

runs/run1/mzlite/preprocessingParams.json

+{
+  "Compress": 0,
+  "StartRetentionTime": null,
+  "EndRetentionTime": null,
+  "MS1PeakPicking": {
+    "Case": "ProfilePeaks"
+  },
+  "MS2PeakPicking": {
+    "Case": "ProfilePeaks"
+  }
+}
\ No newline at end of file

runs/run1/prot/ProteinInferenceParams.json

+{
+  "ProteinIdentifierRegex": "id",
+  "Protein": {
+    "Case": "Maximal"
+  },
+  "Peptide": {
+    "Case": "Minimal"
+  },
+  "GroupFiles": true,
+  "GetQValue": {
+    "Case": "Storey"
+  }
+}
\ No newline at end of file

runs/run1/prot/ProteinInference_createClassItemCollection_log.txt

+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 

runs/run1/prot/ProteinInference_inferProteins_log.txt

+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 

runs/run1/prot/ProteinInference_log.txt

+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"|] 

runs/run1/prot/ProteinInference_readAndInferFile_log.txt

+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