diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..dfcfd56f444f9ae40e1082c07fe254cc547136cf
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,350 @@
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+##
+## Get latest from https://github.com/github/gitignore/blob/master/VisualStudio.gitignore
+
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+mono_crash.*
+
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+
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+.vs/
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+#wwwroot/
+
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+Generated\ Files/
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+
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+
+# Chutzpah Test files
+_Chutzpah*
+
+# Visual C++ cache files
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+# Visual Studio Trace Files
+*.e2e
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+
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+
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+# Note: Comment the next line if you want to checkin your web deploy settings,
+# but database connection strings (with potential passwords) will be unencrypted
+*.pubxml
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+
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+# checkin your Azure Web App publish settings, but sensitive information contained
+# in these scripts will be unencrypted
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+
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+
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+rcf/
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+Package.StoreAssociation.xml
+_pkginfo.txt
+*.appx
+*.appxbundle
+*.appxupload
+
+# Visual Studio cache files
+# files ending in .cache can be ignored
+*.[Cc]ache
+# but keep track of directories ending in .cache
+!?*.[Cc]ache/
+
+# Others
+ClientBin/
+~$*
+*~
+*.dbmdl
+*.dbproj.schemaview
+*.jfm
+*.pfx
+*.publishsettings
+orleans.codegen.cs
+
+# Including strong name files can present a security risk
+# (https://github.com/github/gitignore/pull/2483#issue-259490424)
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+
+# Since there are multiple workflows, uncomment next line to ignore bower_components
+# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
+#bower_components/
+
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+Generated_Code/
+
+# Backup & report files from converting an old project file
+# to a newer Visual Studio version. Backup files are not needed,
+# because we have git ;-)
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+Backup*/
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+# Business Intelligence projects
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+*- [Bb]ackup.rdl
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+*- [Bb]ackup ([0-9][0-9]).rdl
+
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+
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+
+# Paket dependency manager
+.paket/paket.exe
+paket-files/
+
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+.fake/
+
+# CodeRush personal settings
+.cr/personal
+
+# Python Tools for Visual Studio (PTVS)
+__pycache__/
+*.pyc
+
+# Cake - Uncomment if you are using it
+# tools/**
+# !tools/packages.config
+
+# Tabs Studio
+*.tss
+
+# Telerik's JustMock configuration file
+*.jmconfig
+
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+# OpenCover UI analysis results
+OpenCover/
+
+# Azure Stream Analytics local run output
+ASALocalRun/
+
+# MSBuild Binary and Structured Log
+*.binlog
+
+# NVidia Nsight GPU debugger configuration file
+*.nvuser
+
+# MFractors (Xamarin productivity tool) working folder
+.mfractor/
+
+# Local History for Visual Studio
+.localhistory/
+
+# BeatPulse healthcheck temp database
+healthchecksdb
+
+# Backup folder for Package Reference Convert tool in Visual Studio 2017
+MigrationBackup/
+
+# Ionide (cross platform F# VS Code tools) working folder
+.ionide/
diff --git a/01Minimal.study.xlsx b/01Minimal.study.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..f5382c2f64793434dc676e7964d553701170905b
Binary files /dev/null and b/01Minimal.study.xlsx differ
diff --git a/assays/assay1/dataset/minimal1.mzlite b/assays/assay1/dataset/minimal1.mzlite
new file mode 100644
index 0000000000000000000000000000000000000000..7e7964cf87aa00d7e8163e665bdea6812695269f
Binary files /dev/null and b/assays/assay1/dataset/minimal1.mzlite differ
diff --git a/assays/assay1/dataset/minimal2.mzlite b/assays/assay1/dataset/minimal2.mzlite
new file mode 100644
index 0000000000000000000000000000000000000000..7e7964cf87aa00d7e8163e665bdea6812695269f
Binary files /dev/null and b/assays/assay1/dataset/minimal2.mzlite differ
diff --git a/assays/assay1/dataset/minimal3.mzlite b/assays/assay1/dataset/minimal3.mzlite
new file mode 100644
index 0000000000000000000000000000000000000000..7e7964cf87aa00d7e8163e665bdea6812695269f
Binary files /dev/null and b/assays/assay1/dataset/minimal3.mzlite differ
diff --git a/assays/assay1/dataset/minimal4.mzlite b/assays/assay1/dataset/minimal4.mzlite
new file mode 100644
index 0000000000000000000000000000000000000000..7e7964cf87aa00d7e8163e665bdea6812695269f
Binary files /dev/null and b/assays/assay1/dataset/minimal4.mzlite differ
diff --git a/assays/assay1/isa.assay.xlsx b/assays/assay1/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..07c7c6bd2b04a93eee90b6e7f97931098c033cbb
Binary files /dev/null and b/assays/assay1/isa.assay.xlsx differ
diff --git a/externals/example.fasta b/externals/example.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..632c89f0ec1988dac5749ca3f370421d12997b94
--- /dev/null
+++ b/externals/example.fasta
@@ -0,0 +1,11 @@
+>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*
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..38ea78bab30230ab8276b375d6fcc4439d2f65eb
Binary files /dev/null and b/isa.investigation.xlsx differ
diff --git a/runs/run1/db/Minimal.db b/runs/run1/db/Minimal.db
new file mode 100644
index 0000000000000000000000000000000000000000..4bfc9531288acc3db472eb762fa22950511a55ef
Binary files /dev/null and b/runs/run1/db/Minimal.db differ
diff --git a/runs/run1/db/PeptideDB_Minimal_log.txt b/runs/run1/db/PeptideDB_Minimal_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c295643802e46540b1009e78c75b1a0264746b58
--- /dev/null
+++ b/runs/run1/db/PeptideDB_Minimal_log.txt
@@ -0,0 +1,71 @@
+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
diff --git a/runs/run1/db/PeptideDB_log.txt b/runs/run1/db/PeptideDB_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fecc58bfe8802fe993b1d25cddf8a0d3f6d48be
--- /dev/null
+++ b/runs/run1/db/PeptideDB_log.txt
@@ -0,0 +1,4 @@
+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"]
diff --git a/runs/run1/db/peptideDBParams.json b/runs/run1/db/peptideDBParams.json
new file mode 100644
index 0000000000000000000000000000000000000000..609fc0363ab899adf11e53dcf337317a1aab73a3
--- /dev/null
+++ b/runs/run1/db/peptideDBParams.json
@@ -0,0 +1 @@
+{"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
diff --git a/runs/run1/isa.run.xlsx b/runs/run1/isa.run.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..8494133abe59d502a559d277a93173ce0dba108a
Binary files /dev/null and b/runs/run1/isa.run.xlsx differ
diff --git a/runs/run1/mzlite/preprocessingParams.json b/runs/run1/mzlite/preprocessingParams.json
new file mode 100644
index 0000000000000000000000000000000000000000..bdd1cf08b25743f00062b67a375e114d2b8b308b
--- /dev/null
+++ b/runs/run1/mzlite/preprocessingParams.json
@@ -0,0 +1,11 @@
+{
+ "Compress": 0,
+ "StartRetentionTime": null,
+ "EndRetentionTime": null,
+ "MS1PeakPicking": {
+ "Case": "ProfilePeaks"
+ },
+ "MS2PeakPicking": {
+ "Case": "ProfilePeaks"
+ }
+}
\ No newline at end of file
diff --git a/runs/run1/prot/ProteinInferenceParams.json b/runs/run1/prot/ProteinInferenceParams.json
new file mode 100644
index 0000000000000000000000000000000000000000..62981036362c77071e33fc4d79d6e961439cd2ce
--- /dev/null
+++ b/runs/run1/prot/ProteinInferenceParams.json
@@ -0,0 +1,13 @@
+{
+ "ProteinIdentifierRegex": "id",
+ "Protein": {
+ "Case": "Maximal"
+ },
+ "Peptide": {
+ "Case": "Minimal"
+ },
+ "GroupFiles": true,
+ "GetQValue": {
+ "Case": "Storey"
+ }
+}
\ No newline at end of file
diff --git a/runs/run1/prot/ProteinInference_createClassItemCollection_log.txt b/runs/run1/prot/ProteinInference_createClassItemCollection_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15b9938e4d164141e9ec73d1b15112ba2e7b1844
--- /dev/null
+++ b/runs/run1/prot/ProteinInference_createClassItemCollection_log.txt
@@ -0,0 +1,3 @@
+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
diff --git a/runs/run1/prot/ProteinInference_inferProteins_log.txt b/runs/run1/prot/ProteinInference_inferProteins_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9082661196d5d0662e1fb19e8507fc7e9c56f7d
--- /dev/null
+++ b/runs/run1/prot/ProteinInference_inferProteins_log.txt
@@ -0,0 +1,13 @@
+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
diff --git a/runs/run1/prot/ProteinInference_log.txt b/runs/run1/prot/ProteinInference_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcbd666e6de39a8cb5b96981e8243eb3cc3a46b8
--- /dev/null
+++ b/runs/run1/prot/ProteinInference_log.txt
@@ -0,0 +1,9 @@
+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"|]
diff --git a/runs/run1/prot/ProteinInference_readAndInferFile_log.txt b/runs/run1/prot/ProteinInference_readAndInferFile_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9dbbf945f58fcbdc5fa853c60ecbef137a6b4fe
--- /dev/null
+++ b/runs/run1/prot/ProteinInference_readAndInferFile_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/prot/minimal.prot b/runs/run1/prot/minimal.prot
new file mode 100644
index 0000000000000000000000000000000000000000..574887377226d1bd7fc3d182ace9bcfd7cb574da
--- /dev/null
+++ b/runs/run1/prot/minimal.prot
@@ -0,0 +1,3 @@
+ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
+Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
+Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
diff --git a/runs/run1/prot/minimal1.prot b/runs/run1/prot/minimal1.prot
new file mode 100644
index 0000000000000000000000000000000000000000..574887377226d1bd7fc3d182ace9bcfd7cb574da
--- /dev/null
+++ b/runs/run1/prot/minimal1.prot
@@ -0,0 +1,3 @@
+ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
+Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
+Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
diff --git a/runs/run1/prot/minimal2.prot b/runs/run1/prot/minimal2.prot
new file mode 100644
index 0000000000000000000000000000000000000000..574887377226d1bd7fc3d182ace9bcfd7cb574da
--- /dev/null
+++ b/runs/run1/prot/minimal2.prot
@@ -0,0 +1,3 @@
+ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
+Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
+Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
diff --git a/runs/run1/prot/minimal3.prot b/runs/run1/prot/minimal3.prot
new file mode 100644
index 0000000000000000000000000000000000000000..574887377226d1bd7fc3d182ace9bcfd7cb574da
--- /dev/null
+++ b/runs/run1/prot/minimal3.prot
@@ -0,0 +1,3 @@
+ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
+Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
+Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
diff --git a/runs/run1/prot/minimal4.prot b/runs/run1/prot/minimal4.prot
new file mode 100644
index 0000000000000000000000000000000000000000..574887377226d1bd7fc3d182ace9bcfd7cb574da
--- /dev/null
+++ b/runs/run1/prot/minimal4.prot
@@ -0,0 +1,3 @@
+ProteinGroup PeptideSequence Class TargetScore DecoyScore QValue
+Cre02.g143307.t1.1 ILVGDIK C1a NaN 0 NaN
+Cre01.g026550.t1.1 ALEVIPR C1a NaN 0 NaN
diff --git a/runs/run1/psm/PeptideSpectrumMatching_log.txt b/runs/run1/psm/PeptideSpectrumMatching_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21e9eef3377bdac6dbc538ff3392add5fe4eb1e2
--- /dev/null
+++ b/runs/run1/psm/PeptideSpectrumMatching_log.txt
@@ -0,0 +1,10 @@
+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
diff --git a/runs/run1/psm/minimal.psm b/runs/run1/psm/minimal.psm
new file mode 100644
index 0000000000000000000000000000000000000000..f2ff0df1d811f12ed35aeeb6854d6c35636c2450
--- /dev/null
+++ b/runs/run1/psm/minimal.psm
@@ -0,0 +1,7 @@
+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
diff --git a/runs/run1/psm/minimal1.psm b/runs/run1/psm/minimal1.psm
new file mode 100644
index 0000000000000000000000000000000000000000..f2ff0df1d811f12ed35aeeb6854d6c35636c2450
--- /dev/null
+++ b/runs/run1/psm/minimal1.psm
@@ -0,0 +1,7 @@
+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
diff --git a/runs/run1/psm/minimal1_log.txt b/runs/run1/psm/minimal1_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98a688dc35124dc5522dc011a44406571c4718d9
--- /dev/null
+++ b/runs/run1/psm/minimal1_log.txt
@@ -0,0 +1,102 @@
+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.
diff --git a/runs/run1/psm/minimal2.psm b/runs/run1/psm/minimal2.psm
new file mode 100644
index 0000000000000000000000000000000000000000..f2ff0df1d811f12ed35aeeb6854d6c35636c2450
--- /dev/null
+++ b/runs/run1/psm/minimal2.psm
@@ -0,0 +1,7 @@
+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
diff --git a/runs/run1/psm/minimal2_log.txt b/runs/run1/psm/minimal2_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a8003541865af09e5039ab22720fad0cdf0e44a
--- /dev/null
+++ b/runs/run1/psm/minimal2_log.txt
@@ -0,0 +1,102 @@
+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.
diff --git a/runs/run1/psm/minimal3.psm b/runs/run1/psm/minimal3.psm
new file mode 100644
index 0000000000000000000000000000000000000000..f2ff0df1d811f12ed35aeeb6854d6c35636c2450
--- /dev/null
+++ b/runs/run1/psm/minimal3.psm
@@ -0,0 +1,7 @@
+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
diff --git a/runs/run1/psm/minimal3_log.txt b/runs/run1/psm/minimal3_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4f650f939e10b1d567694b76313cb75b2b1e623
--- /dev/null
+++ b/runs/run1/psm/minimal3_log.txt
@@ -0,0 +1,102 @@
+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.
diff --git a/runs/run1/psm/minimal4.psm b/runs/run1/psm/minimal4.psm
new file mode 100644
index 0000000000000000000000000000000000000000..f2ff0df1d811f12ed35aeeb6854d6c35636c2450
--- /dev/null
+++ b/runs/run1/psm/minimal4.psm
@@ -0,0 +1,7 @@
+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
diff --git a/runs/run1/psm/minimal4_log.txt b/runs/run1/psm/minimal4_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e11a975272c511e18205025e65ce82277dbf13a2
--- /dev/null
+++ b/runs/run1/psm/minimal4_log.txt
@@ -0,0 +1,102 @@
+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.
diff --git a/runs/run1/psm/minimal_log.txt b/runs/run1/psm/minimal_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08d870ed25e9f67c7fd5ee08dca985ccf8d75e9f
--- /dev/null
+++ b/runs/run1/psm/minimal_log.txt
@@ -0,0 +1,102 @@
+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.
diff --git a/runs/run1/psm/peptideSpectrumMatchingParams.json b/runs/run1/psm/peptideSpectrumMatchingParams.json
new file mode 100644
index 0000000000000000000000000000000000000000..16ac163ab982a957ca91de16f061ba495cdb1f25
--- /dev/null
+++ b/runs/run1/psm/peptideSpectrumMatchingParams.json
@@ -0,0 +1 @@
+{"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}}
diff --git a/runs/run1/psmstats/PSMStatistics_log.txt b/runs/run1/psmstats/PSMStatistics_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0a9989baf4e9719f8ec755fdcc51bf0d3f47688
--- /dev/null
+++ b/runs/run1/psmstats/PSMStatistics_log.txt
@@ -0,0 +1,10 @@
+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
diff --git a/runs/run1/psmstats/minimal.qpsm b/runs/run1/psmstats/minimal.qpsm
new file mode 100644
index 0000000000000000000000000000000000000000..3ed648b663846740c804df72fbeda27465e23494
--- /dev/null
+++ b/runs/run1/psmstats/minimal.qpsm
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/psmstats/minimal1.qpsm b/runs/run1/psmstats/minimal1.qpsm
new file mode 100644
index 0000000000000000000000000000000000000000..3ed648b663846740c804df72fbeda27465e23494
--- /dev/null
+++ b/runs/run1/psmstats/minimal1.qpsm
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/psmstats/minimal1_log.txt b/runs/run1/psmstats/minimal1_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc8ed3d7eecdf76185a38fd5bf6200fcd4b1655d
--- /dev/null
+++ b/runs/run1/psmstats/minimal1_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/psmstats/minimal2.qpsm b/runs/run1/psmstats/minimal2.qpsm
new file mode 100644
index 0000000000000000000000000000000000000000..3ed648b663846740c804df72fbeda27465e23494
--- /dev/null
+++ b/runs/run1/psmstats/minimal2.qpsm
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/psmstats/minimal2_log.txt b/runs/run1/psmstats/minimal2_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d7eb226375df82a2178fd18af80faf82f3ff2e0
--- /dev/null
+++ b/runs/run1/psmstats/minimal2_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/psmstats/minimal3.qpsm b/runs/run1/psmstats/minimal3.qpsm
new file mode 100644
index 0000000000000000000000000000000000000000..3ed648b663846740c804df72fbeda27465e23494
--- /dev/null
+++ b/runs/run1/psmstats/minimal3.qpsm
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/psmstats/minimal3_log.txt b/runs/run1/psmstats/minimal3_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4960bdb9961047a1e830b1a8340844391fed2444
--- /dev/null
+++ b/runs/run1/psmstats/minimal3_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/psmstats/minimal4.qpsm b/runs/run1/psmstats/minimal4.qpsm
new file mode 100644
index 0000000000000000000000000000000000000000..3ed648b663846740c804df72fbeda27465e23494
--- /dev/null
+++ b/runs/run1/psmstats/minimal4.qpsm
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/psmstats/minimal4_log.txt b/runs/run1/psmstats/minimal4_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f7abe635d6fc18b868e60101e3138d46a7a32df
--- /dev/null
+++ b/runs/run1/psmstats/minimal4_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/psmstats/minimal_log.txt b/runs/run1/psmstats/minimal_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9987c7b7c73a918869ddd7dd1b29a983e26be80
--- /dev/null
+++ b/runs/run1/psmstats/minimal_log.txt
@@ -0,0 +1,16 @@
+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
diff --git a/runs/run1/psmstats/pSMStatisticsParamsFixed.json b/runs/run1/psmstats/pSMStatisticsParamsFixed.json
new file mode 100644
index 0000000000000000000000000000000000000000..1023ebb513eb7b3296816c896af649354796750b
--- /dev/null
+++ b/runs/run1/psmstats/pSMStatisticsParamsFixed.json
@@ -0,0 +1 @@
+{"Threshold":{"Case":"Fixed","Fields":[{"SequestLike":5.0,"Andromeda":40.0}]},"ParseProteinIDRegexPattern":"id","KeepTemporaryFiles":true}
\ No newline at end of file
diff --git a/runs/run1/quant/PSMBasedQuantification_log.txt b/runs/run1/quant/PSMBasedQuantification_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e455b26cca36179559b1616df2fdb6741ac75a23
--- /dev/null
+++ b/runs/run1/quant/PSMBasedQuantification_log.txt
@@ -0,0 +1,14 @@
+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
diff --git a/runs/run1/quant/QuantificationParams.json b/runs/run1/quant/QuantificationParams.json
new file mode 100644
index 0000000000000000000000000000000000000000..82d4662986d91134c203da855664d8779a67b038
--- /dev/null
+++ b/runs/run1/quant/QuantificationParams.json
@@ -0,0 +1 @@
+{"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}]}}
\ No newline at end of file
diff --git a/runs/run1/quant/minimal.quant b/runs/run1/quant/minimal.quant
new file mode 100644
index 0000000000000000000000000000000000000000..29c618e10715d5fa92d398df1f1a3a6644007fc5
--- /dev/null
+++ b/runs/run1/quant/minimal.quant
@@ -0,0 +1,4 @@
+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
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diff --git a/runs/run1/quant/minimal1.quant b/runs/run1/quant/minimal1.quant
new file mode 100644
index 0000000000000000000000000000000000000000..ad372bb9b86ea2c8a4621d1ebc9a559532076b32
--- /dev/null
+++ b/runs/run1/quant/minimal1.quant
@@ -0,0 +1,4 @@
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+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
diff --git a/runs/run1/quant/minimal1_log.txt b/runs/run1/quant/minimal1_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dbedc7c07d1dde92555aef81b5c4cdfda54b4e44
--- /dev/null
+++ b/runs/run1/quant/minimal1_log.txt
@@ -0,0 +1,46 @@
+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
diff --git a/runs/run1/quant/minimal2.quant b/runs/run1/quant/minimal2.quant
new file mode 100644
index 0000000000000000000000000000000000000000..29c618e10715d5fa92d398df1f1a3a6644007fc5
--- /dev/null
+++ b/runs/run1/quant/minimal2.quant
@@ -0,0 +1,4 @@
+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
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+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
diff --git a/runs/run1/quant/minimal2_log.txt b/runs/run1/quant/minimal2_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e80805a70c54ee40f91001ffd717a63360dd5e3f
--- /dev/null
+++ b/runs/run1/quant/minimal2_log.txt
@@ -0,0 +1,46 @@
+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
diff --git a/runs/run1/quant/minimal3.quant b/runs/run1/quant/minimal3.quant
new file mode 100644
index 0000000000000000000000000000000000000000..29c618e10715d5fa92d398df1f1a3a6644007fc5
--- /dev/null
+++ b/runs/run1/quant/minimal3.quant
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/quant/minimal3_log.txt b/runs/run1/quant/minimal3_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc1e2874f5815f74815727486e7fae77cb07aeb6
--- /dev/null
+++ b/runs/run1/quant/minimal3_log.txt
@@ -0,0 +1,46 @@
+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
diff --git a/runs/run1/quant/minimal4.quant b/runs/run1/quant/minimal4.quant
new file mode 100644
index 0000000000000000000000000000000000000000..ad372bb9b86ea2c8a4621d1ebc9a559532076b32
--- /dev/null
+++ b/runs/run1/quant/minimal4.quant
@@ -0,0 +1,4 @@
+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
diff --git a/runs/run1/quant/minimal4_log.txt b/runs/run1/quant/minimal4_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd922b6b108282e35651bf91be792a08b3564611
--- /dev/null
+++ b/runs/run1/quant/minimal4_log.txt
@@ -0,0 +1,46 @@
+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
diff --git a/runs/run1/quant/minimal_log.txt b/runs/run1/quant/minimal_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5acf9af72fe0f264f94f2ccf0346fe89977cbd9c
--- /dev/null
+++ b/runs/run1/quant/minimal_log.txt
@@ -0,0 +1,46 @@
+2021-09-07 09:57:30.4430 minimal TRACE Input file: /FuNLno/mzlite/minimal.mzlite
+2021-09-07 09:57:30.4508 minimal TRACE Output directory: /FuNLno/quant
+2021-09-07 09:57:30.4618 minimal 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 } }
+2021-09-07 09:57:30.4717 minimal TRACE Now performing Quantification using: /FuNLno/mzlite/minimal.mzlite and /FuNLno/psmstats/minimal.qpsm, Results will be written to: /FuNLno/quant
+2021-09-07 09:57:30.4789 minimal TRACE outFilePath:/FuNLno/quant/minimal.quant
+2021-09-07 09:57:30.4921 minimal TRACE plotDirectory:/FuNLno/quant/minimal_plots
+2021-09-07 09:57:30.4921 minimal TRACE Copy peptide DB into Memory
+2021-09-07 09:57:30.5098 minimal TRACE Copy peptide DB into Memory: finished
+2021-09-07 09:57:30.5098 minimal TRACE Get peptide lookUp function
+2021-09-07 09:57:30.5814 minimal TRACE Get peptide lookUp function: finished
+2021-09-07 09:57:30.5814 minimal TRACE Init connection to mass spectrum data.
+2021-09-07 09:57:30.6131 minimal TRACE Create RetentionTime index
+2021-09-07 09:57:30.7196 minimal TRACE Create RetentionTime index:finished
+2021-09-07 09:57:30.7287 minimal TRACE Read and sort ms1s
+2021-09-07 09:57:30.7657 minimal TRACE Read and sort ms1s:finished
+2021-09-07 09:57:30.7757 minimal TRACE Read scored PSMs
+2021-09-07 09:57:30.8056 minimal TRACE Read scored PSMs:finished
+2021-09-07 09:57:30.8141 minimal TRACE Estimate precursor mz standard deviation and mz correction.
+2021-09-07 09:57:30.8309 minimal TRACE Estimate precursor mz standard deviation and mz correction.:finished, standard deviation: 0.000920
+2021-09-07 09:57:30.8411 minimal TRACE init lookup functions
+2021-09-07 09:57:30.8459 minimal TRACE init lookup functions:finished
+2021-09-07 09:57:30.8459 minimal TRACE init quantification functions
+2021-09-07 09:57:30.8459 minimal TRACE init quantification functions:finished
+2021-09-07 09:57:30.8579 minimal TRACE executing quantification
+2021-09-07 09:57:30.8670 minimal TRACE 0 peptides quantified
+2021-09-07 09:57:31.2593 minimal TRACE executing quantification:finished
diff --git a/runs/run1/run.cwl b/runs/run1/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e6d0afb1db514b48a528716b1c5f4aa0c2c2501b
--- /dev/null
+++ b/runs/run1/run.cwl
@@ -0,0 +1,97 @@
+
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+ MultipleInputFeatureRequirement: {}
+
+inputs:
+ cores: int
+ outputDB: string
+ outputMzML: string
+ outputPSM: string
+ outputPSMStats: string
+ outputQuant: string
+ outputProt: string
+ inputDB: File
+ inputPSM: Directory
+ paramsDB: File
+ paramsMzML: File
+ paramsPSM: File
+ paramsPSMStats: File
+ paramsPSMBasedQuant: File
+ paramsProt: File
+
+steps:
+ #MzMLToMzlite:
+ # run: ./../../workflows/MzMLToMzlite/proteomiqon-mzmltomzlite.cwl
+ # in:
+ # stageDirectory: stage
+ # inputDirectory: inputMzML
+ # params: paramsMzML
+ # outputDirectory: outputMzML
+ # parallelismLevel: cores
+ # out: [dir]
+ PeptideDB:
+ run: ./../../workflows/PeptideDB/proteomiqon-peptidedb.cwl
+ in:
+ inputFile: inputDB
+ params: paramsDB
+ outputDirectory: outputDB
+ out: [db, dbFolder]
+ PeptideSpectrumMatching:
+ run: ./../../workflows/PeptideSpectrumMatching/proteomiqon-peptidespectrummatching.cwl
+ in:
+ inputDirectory: inputPSM
+ database: PeptideDB/db
+ params: paramsPSM
+ outputDirectory: outputPSM
+ parallelismLevel: cores
+ out: [dir]
+ PSMStatistics:
+ run: ./../../workflows/PSMStatistics/proteomiqon-psmstatistics.cwl
+ in:
+ inputDirectory: PeptideSpectrumMatching/dir
+ database: PeptideDB/db
+ params: paramsPSMStats
+ outputDirectory: outputPSMStats
+ parallelismLevel: cores
+ out: [dir]
+ PSMBasedQuantification:
+ run: ./../../workflows/PSMBasedQuantification/proteomiqon-psmbasedquantification.cwl
+ in:
+ inputDirectoryI: inputPSM
+ inputDirectoryII: PSMStatistics/dir
+ database: PeptideDB/db
+ params: paramsPSMBasedQuant
+ outputDirectory: outputQuant
+ parallelismLevel: cores
+ out: [dir]
+ ProteinInference:
+ run: ./../../workflows/ProteinInference/proteomiqon-proteininference.cwl
+ in:
+ inputDirectory: PSMStatistics/dir
+ database: PeptideDB/db
+ params: paramsProt
+ outputDirectory: outputProt
+ out: [dir]
+
+outputs:
+ #mzlite:
+ # type: Directory
+ # outputSource: MzMLToMzlite/dir
+ peptidedb:
+ type: Directory
+ outputSource: PeptideDB/dbFolder
+ psm:
+ type: Directory
+ outputSource: PeptideSpectrumMatching/dir
+ psmStats:
+ type: Directory
+ outputSource: PSMStatistics/dir
+ quant:
+ type: Directory
+ outputSource: PSMBasedQuantification/dir
+ prot:
+ type: Directory
+ outputSource: ProteinInference/dir
\ No newline at end of file
diff --git a/runs/run1/run.yml b/runs/run1/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..df11e12fbacbe2b2dd852e59ab46014e7ee77cc9
--- /dev/null
+++ b/runs/run1/run.yml
@@ -0,0 +1,31 @@
+cores: 1
+outputDB: db
+outputMzML: mzlite
+outputPSM: psm
+outputPSMStats: psmstats
+outputQuant: quant
+outputProt: prot
+inputDB:
+ class: File
+ path: ./../../externals/example.fasta
+inputPSM:
+ class: Directory
+ path: ./../../assays/assay1/dataset
+paramsDB:
+ class: File
+ path: ./db/peptideDBParams.json
+paramsMzML:
+ class: File
+ path: ./mzlite/preprocessingParams.json
+paramsPSM:
+ class: File
+ path: ./psm/peptideSpectrumMatchingParams.json
+paramsPSMStats:
+ class: File
+ path: ./psmstats/pSMStatisticsParamsFixed.json
+paramsPSMBasedQuant:
+ class: File
+ path: ./quant/QuantificationParams.json
+paramsProt:
+ class: File
+ path: ./prot/ProteinInferenceParams.json
\ No newline at end of file
diff --git a/workflows/MzMLToMzlite/Dockerfile b/workflows/MzMLToMzlite/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..7063a7ab0b89d250c319f4a224e8b000f8c60f5d
--- /dev/null
+++ b/workflows/MzMLToMzlite/Dockerfile
@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool in $HOME/.dotnet/tools
+RUN dotnet tool install \
+ ProteomIQon.MzMLToMzLite \
+ --version 0.0.6 \
+ --tool-path /usr/local/bin
\ No newline at end of file
diff --git a/workflows/MzMLToMzlite/proteomiqon-mzmltomzlite.cwl b/workflows/MzMLToMzlite/proteomiqon-mzmltomzlite.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..043bcda8e4801c1b300924fdcbedccbda569000d
--- /dev/null
+++ b/workflows/MzMLToMzlite/proteomiqon-mzmltomzlite.cwl
@@ -0,0 +1,51 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: mzmltomzlite
+ dockerFile:
+ $include: ./Dockerfile
+baseCommand: ['proteomiqon-mzmltomzlite']
+inputs:
+ # inputtype that declares the directory to be staged?
+ stageDirectory:
+ type: Directory
+ inputDirectory:
+ type: Directory
+ inputBinding:
+ position: 1
+ prefix: -i
+ params:
+ type: File
+ inputBinding:
+ position: 2
+ prefix: -p
+ outputDirectory:
+ type: Directory
+ inputBinding:
+ position: 3
+ prefix: -o
+ parallelismLevel:
+ type: int
+ inputBinding:
+ position: 4
+ prefix: -c
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.inputDirectory)
+ writable: true
+ #- entry: $(inputs.stageDirectory)
+ # writable: true
+ - entry: $(inputs.outputDirectory)
+ writable: true
+outputs:
+ dir:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory.basename)
+
+
+
diff --git a/workflows/PSMBasedQuantification/Dockerfile b/workflows/PSMBasedQuantification/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..8da8bda2b4178a0508b1fa4ece4bc87c7a89586c
--- /dev/null
+++ b/workflows/PSMBasedQuantification/Dockerfile
@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool in $HOME/.dotnet/tools
+RUN dotnet tool install \
+ ProteomIQon.PSMBasedQuantification \
+ --version 0.0.7 \
+ --tool-path /usr/local/bin
diff --git a/workflows/PSMBasedQuantification/proteomiqon-psmbasedquantification.cwl b/workflows/PSMBasedQuantification/proteomiqon-psmbasedquantification.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..75bdfe66165908d4b9d9b7ded64a5fd054ed76ba
--- /dev/null
+++ b/workflows/PSMBasedQuantification/proteomiqon-psmbasedquantification.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: psmbasedquantification
+ dockerFile:
+ $include: ./Dockerfile
+baseCommand: ['proteomiqon-psmbasedquantification']
+inputs:
+ inputDirectoryI:
+ type: Directory
+ inputBinding:
+ position: 1
+ prefix: -i
+ inputDirectoryII:
+ type: Directory
+ inputBinding:
+ position: 2
+ prefix: -ii
+ database:
+ type: File
+ inputBinding:
+ position: 3
+ prefix: -d
+ params:
+ type: File
+ inputBinding:
+ position: 4
+ prefix: -p
+ outputDirectory:
+ type: string
+ inputBinding:
+ position: 5
+ prefix: -o
+ parallelismLevel:
+ type: int
+ inputBinding:
+ position: 6
+ prefix: -c
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.inputDirectoryI)
+ writable: true
+ - entry: $(inputs.inputDirectoryII)
+ writable: true
+ - entry: "$({class: 'Directory', listing: []})"
+ entryname: inputs.OutputDirectory
+ writable: true
+outputs:
+ dir:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory)
+
+
+
+
diff --git a/workflows/PSMStatistics/Dockerfile b/workflows/PSMStatistics/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..ab758bcc0a80d0720a0d41b0906c45ebd800f530
--- /dev/null
+++ b/workflows/PSMStatistics/Dockerfile
@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool in $HOME/.dotnet/tools
+RUN dotnet tool install \
+ ProteomIQon.PSMStatistics \
+ --version 0.0.7 \
+ --tool-path /usr/local/bin
\ No newline at end of file
diff --git a/workflows/PSMStatistics/proteomiqon-psmstatistics.cwl b/workflows/PSMStatistics/proteomiqon-psmstatistics.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..2454043ecb2a1fa25bd3ddb9b03b0db4f7c197bf
--- /dev/null
+++ b/workflows/PSMStatistics/proteomiqon-psmstatistics.cwl
@@ -0,0 +1,50 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: psmstatistics
+ dockerFile:
+ $include: ./Dockerfile
+baseCommand: ['proteomiqon-psmstatistics']
+inputs:
+ inputDirectory:
+ type: Directory
+ inputBinding:
+ position: 1
+ prefix: -i
+ database:
+ type: File
+ inputBinding:
+ position: 2
+ prefix: -d
+ params:
+ type: File
+ inputBinding:
+ position: 3
+ prefix: -p
+ outputDirectory:
+ type: string
+ inputBinding:
+ position: 4
+ prefix: -o
+ parallelismLevel:
+ type: int
+ inputBinding:
+ position: 5
+ prefix: -c
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.inputDirectory)
+ writable: true
+ - entry: "$({class: 'Directory', listing: []})"
+ entryname: inputs.OutputDirectory
+ writable: true
+outputs:
+ dir:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory)
diff --git a/workflows/PeptideDB/Dockerfile b/workflows/PeptideDB/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..2b1277d901c03538858d454307274bc4fbc078f5
--- /dev/null
+++ b/workflows/PeptideDB/Dockerfile
@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool in $HOME/.dotnet/tools
+RUN dotnet tool install \
+ ProteomIQon.PeptideDB \
+ --version 0.0.7 \
+ --tool-path /usr/local/bin
\ No newline at end of file
diff --git a/workflows/PeptideDB/proteomiqon-peptidedb.cwl b/workflows/PeptideDB/proteomiqon-peptidedb.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..ccc88eac145aa2f28ddca88aa744c078219f5f03
--- /dev/null
+++ b/workflows/PeptideDB/proteomiqon-peptidedb.cwl
@@ -0,0 +1,45 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: peptidedb
+ dockerFile:
+ $include: ./Dockerfile
+baseCommand: ['proteomiqon-peptidedb']
+inputs:
+ inputFile:
+ type: File
+ inputBinding:
+ position: 1
+ prefix: -i
+ params:
+ type: File
+ inputBinding:
+ position: 2
+ prefix: -p
+ outputDirectory:
+ type: string
+ inputBinding:
+ position: 3
+ prefix: -o
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: "$({class: 'Directory', listing: []})"
+ entryname: inputs.outputDirectory
+ writable: true
+outputs:
+ db:
+ type: File
+ outputBinding:
+ glob: "*/*.db"
+ dbFolder:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory)
+
+
+
diff --git a/workflows/PeptideSpectrumMatching/Dockerfile b/workflows/PeptideSpectrumMatching/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..2fa1098ecdee64858826c09e4b07cc117c61aaea
--- /dev/null
+++ b/workflows/PeptideSpectrumMatching/Dockerfile
@@ -0,0 +1,8 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool
+RUN dotnet tool install \
+ ProteomIQon.PeptideSpectrumMatching \
+ --version 0.0.7 \
+ --tool-path /usr/local/bin
+
diff --git a/workflows/PeptideSpectrumMatching/proteomiqon-peptidespectrummatching.cwl b/workflows/PeptideSpectrumMatching/proteomiqon-peptidespectrummatching.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..f50cf0454a6caafe9c67f557dd5f4b8aad18c71d
--- /dev/null
+++ b/workflows/PeptideSpectrumMatching/proteomiqon-peptidespectrummatching.cwl
@@ -0,0 +1,55 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: peptidespectrummatching
+ dockerFile:
+ $include: ./Dockerfile
+
+baseCommand: [ 'proteomiqon-peptidespectrummatching' ]
+
+inputs:
+ inputDirectory:
+ type: Directory
+ inputBinding:
+ position: 1
+ prefix: -i
+ database:
+ type: File
+ inputBinding:
+ position: 2
+ prefix: -d
+ params:
+ type: File
+ inputBinding:
+ position: 3
+ prefix: -p
+ outputDirectory:
+ type: string
+ inputBinding:
+ position: 4
+ prefix: -o
+ parallelismLevel:
+ type: int
+ inputBinding:
+ position: 5
+ prefix: -c
+
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.inputDirectory)
+ writable: true
+ - entry: "$({class: 'Directory', listing: []})"
+ entryname: inputs.outputDirectory
+ writable: true
+
+outputs:
+ dir:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory)
+
diff --git a/workflows/ProteinInference/Dockerfile b/workflows/ProteinInference/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..8a40bdb9b26a905f2138cef795dbce9059e7cc41
--- /dev/null
+++ b/workflows/ProteinInference/Dockerfile
@@ -0,0 +1,7 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0
+
+# Install tool in $HOME/.dotnet/tools
+RUN dotnet tool install \
+ ProteomIQon.ProteinInference \
+ --version 0.0.7 \
+ --tool-path /usr/local/bin
\ No newline at end of file
diff --git a/workflows/ProteinInference/proteomiqon-proteininference.cwl b/workflows/ProteinInference/proteomiqon-proteininference.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4ed9b0036d8c02f93e9dc3e7722b46a196b529b4
--- /dev/null
+++ b/workflows/ProteinInference/proteomiqon-proteininference.cwl
@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: proteininference
+ dockerFile:
+ $include: ./Dockerfile
+baseCommand: ['proteomiqon-proteininference']
+inputs:
+ inputDirectory:
+ type: Directory
+ inputBinding:
+ position: 1
+ prefix: -i
+ database:
+ type: File
+ inputBinding:
+ position: 2
+ prefix: -d
+ params:
+ type: File
+ inputBinding:
+ position: 3
+ prefix: -p
+ outputDirectory:
+ type: string
+ inputBinding:
+ position: 4
+ prefix: -o
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.inputDirectory)
+ writable: true
+ - entry: "$({class: 'Directory', listing: []})"
+ entryname: inputs.outputDirectory
+ writable: true
+outputs:
+ dir:
+ type: Directory
+ outputBinding:
+ glob: $(inputs.outputDirectory)
+
+
+
+