diff --git a/Changelog b/Changelog
index 54b99c0d..99b51783 100644
--- a/Changelog
+++ b/Changelog
@@ -1,4 +1,8 @@
+### Added
+- FASTA header verification for IonQuant
+
+### Changed
+- New version annoucements will happpen for all updates, including minor changes
+
 ### Fixed
-- Fixed the protein coverage calculations with partially overlapping and subsumed peptides
-- Fixed an issue where peptides would map to multiple locations in the protein after having I/L converted (Needs to be used with MSFragger v3.6.1 or higher)
-- Fixed an issue with report tables having no isobaric labels being reported
\ No newline at end of file
+- Fixed an issue that would not udpate PSMs with razor IDs and description
\ No newline at end of file
diff --git a/Makefile b/Makefile
index c07ce4e3..4578d9b7 100644
--- a/Makefile
+++ b/Makefile
@@ -6,8 +6,8 @@ BINARY = philosopher
 VERSION = $(shell date +%Y%m%d)
 BUILD = $(shell  date +%Y%m%d%H%M)
 
-TAG = v4.8.0
-RC = RC
+TAG = v4.8.1
+RC = RC2
 
 LDFLAGS = -ldflags "-w -s -extldflags -static -X main.version=${TAG} -X main.build=${BUILD}"
 
diff --git a/lib/aba/aba.go b/lib/aba/aba.go
index be693988..ba402b9b 100644
--- a/lib/aba/aba.go
+++ b/lib/aba/aba.go
@@ -12,13 +12,8 @@ type DataSetLabelNames struct {
 }
 
 // Run abacus
-// TODO update error methos on the abacus function
 func Run(m met.Data, args []string) {
 
-	// if !m.Abacus.Peptide && !m.Abacus.Protein {
-	// 	msg.Custom(errors.New("you need to specify a peptide or protein combined file for the Abacus analysis"), "fatal")
-	// }
-
 	psmLevelAbacus(m, args)
 
 	if m.Abacus.Peptide {
@@ -29,30 +24,3 @@ func Run(m met.Data, args []string) {
 		proteinLevelAbacus(m, args)
 	}
 }
-
-// addCustomNames adds to the label structures user-defined names to be used on the TMT labels
-// func getLabelNames(dataSet, annot string) map[string]string {
-
-// 	var labels = make(map[string]string)
-
-// 	file, e := os.Open(annot)
-// 	if e != nil {
-// 		msg.ReadFile(errors.New("cannot open annotation file"), "error")
-// 	}
-// 	defer file.Close()
-
-// 	scanner := bufio.NewScanner(file)
-// 	for scanner.Scan() {
-// 		names := strings.Fields(scanner.Text())
-
-// 		name := dataSet + " " + names[0]
-
-// 		labels[name] = names[1]
-// 	}
-
-// 	if e = scanner.Err(); e != nil {
-// 		msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
-// 	}
-
-// 	return labels
-// }
diff --git a/lib/aba/pep.go b/lib/aba/pep.go
index f231c5f6..3e093f6b 100644
--- a/lib/aba/pep.go
+++ b/lib/aba/pep.go
@@ -54,17 +54,13 @@ func peptideLevelAbacus(m met.Data, args []string) {
 
 		// collect interact full file names
 		for _, f := range files {
-			//if strings.Contains(f.Name(), "pep.xml") {
-			//interactFile := fmt.Sprintf("%s%s%s", i, string(filepath.Separator), f.Name())
-			//absPath, _ := filepath.Abs(interactFile)
-			//xmlFiles = append(xmlFiles, absPath)
-			//}
+
 			if strings.Contains(f.Name(), "annotation") {
 				var annot = fmt.Sprintf("%s%s%s", i, string(filepath.Separator), f.Name())
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -78,7 +74,7 @@ func peptideLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 
@@ -117,7 +113,7 @@ func processPeptideCombinedFile(a met.Abacus) {
 
 	if _, e := os.Stat("combined.pep.xml"); os.IsNotExist(e) {
 
-		msg.NoParametersFound(errors.New("cannot find the combined.pep.xml file"), "fatal")
+		msg.NoParametersFound(errors.New("cannot find the combined.pep.xml file"), "error")
 
 	} else {
 
@@ -272,7 +268,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -286,7 +282,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 	line += "\n"
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -328,7 +324,7 @@ func savePeptideAbacusResult(session string, evidences rep.CombinedPeptideEviden
 		line += "\n"
 		_, e = io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
diff --git a/lib/aba/pro.go b/lib/aba/pro.go
index 5c184362..640ba7fc 100644
--- a/lib/aba/pro.go
+++ b/lib/aba/pro.go
@@ -60,7 +60,7 @@ func proteinLevelAbacus(m met.Data, args []string) {
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -74,7 +74,7 @@ func proteinLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 		}
@@ -157,7 +157,7 @@ func processProteinCombinedFile(a met.Abacus, database dat.Base) rep.CombinedPro
 
 	if _, e := os.Stat("combined.prot.xml"); os.IsNotExist(e) {
 
-		msg.Custom(errors.New("cannot find combined.prot.xml file"), "fatal")
+		msg.Custom(errors.New("cannot find combined.prot.xml file"), "error")
 
 	} else {
 
@@ -409,7 +409,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -464,7 +464,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	} else if plex == "18" {
 		chs = append(chs, "126", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N", "134C", "135N")
 	} else {
-		msg.Custom(errors.New("unsupported number of labels"), "fatal")
+		msg.Custom(errors.New("unsupported number of labels"), "error")
 	}
 
 	if hasLabels {
@@ -486,7 +486,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 	header += "\n"
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range evidences {
@@ -631,7 +631,7 @@ func saveProteinAbacusResult(session, plex string, evidences rep.CombinedProtein
 			line += "\n"
 			_, e := io.WriteString(file, line)
 			if e != nil {
-				msg.WriteToFile(e, "fatal")
+				msg.WriteToFile(e, "error")
 			}
 
 		}
@@ -651,7 +651,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create reprint SpC report"), "error")
+		msg.WriteFile(errors.New("cannot create reprint SpC report"), "fatal")
 	}
 	defer file.Close()
 
@@ -672,7 +672,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -691,7 +691,7 @@ func saveReprintSpCResults(session, plex string, evidences rep.CombinedProteinEv
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
@@ -710,7 +710,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create reprint Int. report"), "error")
+		msg.WriteFile(errors.New("cannot create reprint Int. report"), "fatal")
 	}
 	defer file.Close()
 
@@ -731,7 +731,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// organize by group number
@@ -750,7 +750,7 @@ func saveReprintIntResults(session, plex string, evidences rep.CombinedProteinEv
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
diff --git a/lib/aba/psm.go b/lib/aba/psm.go
index ceb6afe2..efbb3431 100644
--- a/lib/aba/psm.go
+++ b/lib/aba/psm.go
@@ -43,7 +43,7 @@ func psmLevelAbacus(m met.Data, args []string) {
 
 				file, e := os.Open(annot)
 				if e != nil {
-					msg.ReadFile(errors.New("cannot open annotation file"), "error")
+					msg.ReadFile(errors.New("cannot open annotation file"), "fatal")
 				}
 				defer file.Close()
 
@@ -57,7 +57,7 @@ func psmLevelAbacus(m met.Data, args []string) {
 				}
 
 				if e = scanner.Err(); e != nil {
-					msg.Custom(errors.New("the annotation file looks to be empty"), "fatal")
+					msg.Custom(errors.New("the annotation file looks to be empty"), "error")
 				}
 			}
 		}
@@ -122,7 +122,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "error")
+		msg.WriteFile(e, "fatal")
 	}
 	defer file.Close()
 
@@ -144,7 +144,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	} else if plex == "18" {
 		chs = append(chs, "126", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N", "131C", "132N", "132C", "133N", "133C", "134N", "134C", "135N")
 	} else {
-		msg.Custom(errors.New("unsupported number of labels"), "fatal")
+		msg.Custom(errors.New("unsupported number of labels"), "error")
 	}
 
 	if hasLabels {
@@ -164,7 +164,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 	header += "\n"
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range evidences {
@@ -267,7 +267,7 @@ func savePSMAbacusResult(session, plex string, evidences rep.CombinedPSMEvidence
 		line += "\n"
 		_, e := io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 	}
 
diff --git a/lib/bio/bio_test.go b/lib/bio/bio_test.go
index 45d92f9d..b3173240 100644
--- a/lib/bio/bio_test.go
+++ b/lib/bio/bio_test.go
@@ -112,13 +112,6 @@ func TestAminoAcids(t *testing.T) {
 
 }
 
-// func TestProtonMass(t *testing.T) {
-// 	p := Proton
-// 	if p != float64(1.007276) {
-// 		t.Errorf("Proton mass is incorrect, got %f, want %f", p, 1.007276)
-// 	}
-// }
-
 func TestEnzymes(t *testing.T) {
 
 	tes.SetupTestEnv()
diff --git a/lib/dat/dat.go b/lib/dat/dat.go
index 0d012411..f0c4aed3 100644
--- a/lib/dat/dat.go
+++ b/lib/dat/dat.go
@@ -56,7 +56,7 @@ func Run(m met.Data) met.Data {
 	var db = New()
 
 	if len(m.Database.ID) == 0 && (len(m.Database.Annot) == 0 || m.Database.Annot == "--contam" || m.Database.Annot == "--prefix") && (len(m.Database.Custom) == 0 || m.Database.Custom == "--contam" || m.Database.Custom == "--prefix") {
-		msg.InputNotFound(errors.New("provide a protein FASTA file or Proteome ID"), "fatal")
+		msg.InputNotFound(errors.New("provide a protein FASTA file or Proteome ID"), "error")
 	}
 
 	if len(m.Database.Annot) > 0 {
@@ -73,7 +73,7 @@ func Run(m met.Data) met.Data {
 	}
 
 	if len(m.Database.ID) < 1 && len(m.Database.Custom) < 1 {
-		msg.InputNotFound(errors.New("you need to provide a taxon ID or a custom FASTA file"), "fatal")
+		msg.InputNotFound(errors.New("you need to provide a taxon ID or a custom FASTA file"), "error")
 	}
 
 	if !m.Database.Crap {
@@ -139,6 +139,11 @@ func (d *Base) ProcessDB(file, decoyTag string) {
 
 		class := Classify(k, decoyTag)
 
+		if strings.Contains(k, "@") {
+			m := "The proteion record [" + k + "] contains an unsupported character: @. Please remove it before running philosopher again"
+			msg.Custom(errors.New(m), "error")
+		}
+
 		if class == "uniprot" {
 
 			db := ProcessUniProtKB(k, v, decoyTag)
@@ -175,7 +180,7 @@ func (d *Base) ProcessDB(file, decoyTag string) {
 			d.Records = append(d.Records, db)
 
 		} else {
-			msg.ParsingFASTA(errors.New(""), "fatal")
+			msg.ParsingFASTA(errors.New(""), "error")
 		}
 	}
 
@@ -241,14 +246,14 @@ func (d *Base) Fetch(uniprotID, proteomeID, temp string, iso, rev bool) {
 	// tries to create an output file
 	output, e := os.Create(d.UniProtDB)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create a local database file"), "fatal")
+		msg.WriteFile(errors.New("cannot create a local database file"), "error")
 	}
 	defer output.Close()
 
 	// tries to download data from Uniprot
 	_, e = io.Copy(output, gz)
 	if e != nil {
-		msg.Custom(errors.New("UniProt download failed, please check your connection"), "fatal")
+		msg.Custom(errors.New("UniProt download failed, please check your connection"), "error")
 	}
 
 	d.DownloadedFiles = append(d.DownloadedFiles, d.UniProtDB)
@@ -327,12 +332,12 @@ func (d *Base) Deploy(temp string) {
 
 	param, e1 := Asset("crap-gpmdb.fas")
 	if e1 != nil {
-		msg.WriteFile(e1, "fatal")
+		msg.WriteFile(e1, "error")
 	}
 
 	e2 := ioutil.WriteFile(d.CrapDB, param, sys.FilePermission())
 	if e2 != nil {
-		msg.WriteFile(e2, "fatal")
+		msg.WriteFile(e2, "error")
 	}
 
 }
@@ -346,12 +351,12 @@ func GetOrganismID(temp string, uniprotID string) (string, string) {
 
 	param, e1 := Asset("proteomes.csv")
 	if e1 != nil {
-		msg.WriteFile(e1, "fatal")
+		msg.WriteFile(e1, "error")
 	}
 
 	e2 := ioutil.WriteFile(proteomeFile, param, sys.FilePermission())
 	if e2 != nil {
-		msg.WriteFile(e2, "fatal")
+		msg.WriteFile(e2, "error")
 	}
 
 	f, e := os.Open(proteomeFile)
@@ -408,7 +413,7 @@ func (d *Base) Save(home, temp, ids, tag string, isRev, hasIso, noD, Crap bool)
 	// create db file
 	file, e := os.Create(workfile)
 	if e != nil {
-		msg.ReadFile(errors.New("cannot open the database file"), "fatal")
+		msg.ReadFile(errors.New("cannot open the database file"), "error")
 	}
 	defer file.Close()
 
@@ -423,7 +428,7 @@ func (d *Base) Save(home, temp, ids, tag string, isRev, hasIso, noD, Crap bool)
 		line := i + "\n" + d.TaDeDB[i] + "\n"
 		_, e = io.WriteString(file, line)
 		if e != nil {
-			msg.WriteFile(e, "fatal")
+			msg.WriteFile(e, "error")
 		}
 	}
 
@@ -437,12 +442,12 @@ func (d *Base) Serialize() {
 
 	b, e := msgpack.Marshal(&d)
 	if e != nil {
-		msg.MarshalFile(e, "fatal")
+		msg.MarshalFile(e, "error")
 	}
 
 	e = ioutil.WriteFile(sys.DBBin(), b, sys.FilePermission())
 	if e != nil {
-		msg.SerializeFile(e, "fatal")
+		msg.SerializeFile(e, "error")
 	}
 
 }
diff --git a/lib/dat/db.go b/lib/dat/db.go
index 03e4cc3e..8df47974 100644
--- a/lib/dat/db.go
+++ b/lib/dat/db.go
@@ -282,7 +282,7 @@ func ProcessUniProtKB(k, v, decoyTag string) Record {
 	if strings.Contains(k, "GN=") && (strings.Contains(k, "PE=") || strings.Contains(k, "SV=")) {
 
 		if len(orn) < 2 {
-			msg.ParsingFASTA(errors.New(""), "fatal")
+			msg.ParsingFASTA(errors.New(""), "error")
 		}
 
 		gnReg := regexp.MustCompile(`GN=(.+?)(\s.+)`)
diff --git a/lib/ext/comet/comet.go b/lib/ext/comet/comet.go
index 41e3fc04..2ad58b37 100644
--- a/lib/ext/comet/comet.go
+++ b/lib/ext/comet/comet.go
@@ -49,7 +49,7 @@ func Run(m met.Data, args []string) met.Data {
 	var cmt = New(m.Temp)
 
 	if len(m.Comet.Param) < 1 || !m.Comet.Print && len(args) < 1 {
-		msg.Comet(errors.New(""), "fatal")
+		msg.Comet(errors.New(""), "error")
 	}
 
 	// deploy the binaries
@@ -69,7 +69,7 @@ func Run(m met.Data, args []string) met.Data {
 	paramAbs, _ := filepath.Abs(m.Comet.Param)
 	binFile, e := ioutil.ReadFile(paramAbs)
 	if e != nil {
-		msg.Custom(e, "fatal")
+		msg.Custom(e, "error")
 	}
 	m.Comet.ParamFile = binFile
 
diff --git a/lib/ext/interprophet/interprophet.go b/lib/ext/interprophet/interprophet.go
index b0bae24a..c950722a 100644
--- a/lib/ext/interprophet/interprophet.go
+++ b/lib/ext/interprophet/interprophet.go
@@ -42,7 +42,7 @@ func Run(m met.Data, args []string) met.Data {
 	m.InterProphet.InputFiles = args
 
 	if len(args) < 1 {
-		msg.NoParametersFound(errors.New("IProphet input files"), "fatal")
+		msg.NoParametersFound(errors.New("IProphet input files"), "error")
 	}
 
 	// deploy the binaries
@@ -90,12 +90,12 @@ func (i InterProphet) Execute(params met.InterProphet, home, temp string, args [
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 	_ = cmd.Wait()
 
 	if cmd.ProcessState.ExitCode() != 0 {
-		msg.ExecutingBinary(errors.New("there was an error with iProphet, please check your parameters and input files"), "fatal")
+		msg.ExecutingBinary(errors.New("there was an error with iProphet, please check your parameters and input files"), "error")
 	}
 
 	// copy to work directory
diff --git a/lib/ext/interprophet/interprophet_unix.go b/lib/ext/interprophet/interprophet_unix.go
index 1f4aba81..2ec7c7f9 100644
--- a/lib/ext/interprophet/interprophet_unix.go
+++ b/lib/ext/interprophet/interprophet_unix.go
@@ -22,6 +22,6 @@ func (i *InterProphet) Deploy(distro string) {
 		unix.UnixInterProphetParser(i.UnixInterProphetParser)
 		i.DefaultInterProphetParser = i.UnixInterProphetParser
 	} else {
-		msg.UnsupportedDistribution(errors.New(""), "fatal")
+		msg.UnsupportedDistribution(errors.New(""), "error")
 	}
 }
diff --git a/lib/ext/msfragger/msfragger.go b/lib/ext/msfragger/msfragger.go
index c63d0cdf..dcdb8489 100644
--- a/lib/ext/msfragger/msfragger.go
+++ b/lib/ext/msfragger/msfragger.go
@@ -42,7 +42,7 @@ func Run(m met.Data, args []string) met.Data {
 		paramAbs, _ := filepath.Abs(m.MSFragger.Param)
 		binFile, e := ioutil.ReadFile(paramAbs)
 		if e != nil {
-			msg.ReadFile(e, "fatal")
+			msg.ReadFile(e, "error")
 		}
 		m.MSFragger.ParamFile = binFile
 	}
@@ -71,7 +71,7 @@ func (c *MSFragger) Execute(params met.MSFragger, cmdArgs []string) {
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 
 	_ = cmd.Wait()
@@ -100,7 +100,7 @@ func (c *MSFragger) ExecutewithParameter(params met.MSFragger, cmdArgs []string)
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 
 	_ = cmd.Wait()
diff --git a/lib/ext/peptideprophet/peptideprophet.go b/lib/ext/peptideprophet/peptideprophet.go
index f3386dbe..33318017 100644
--- a/lib/ext/peptideprophet/peptideprophet.go
+++ b/lib/ext/peptideprophet/peptideprophet.go
@@ -52,7 +52,7 @@ func Run(m met.Data, args []string) met.Data {
 	var pep = New(m.Temp)
 
 	// if len(m.PeptideProphet.Database) < 1 {
-	// 	msg.Custom(errors.New("You need to provide a protein database"), "fatal")
+	// 	msg.Custom(errors.New("You need to provide a protein database"), "error")
 	// }
 
 	// get the database tag from database command
@@ -165,7 +165,7 @@ func interactParser(p PeptideProphet, params met.PeptideProphet, home, temp stri
 			cmd.Stderr = os.Stderr
 			e := cmd.Start()
 			if e != nil {
-				msg.ExecutingBinary(e, "fatal")
+				msg.ExecutingBinary(e, "error")
 			}
 			_ = cmd.Wait()
 
@@ -221,18 +221,18 @@ func interactParser(p PeptideProphet, params met.PeptideProphet, home, temp stri
 
 		e := cmd.Start()
 		if e != nil {
-			msg.ExecutingBinary(e, "fatal")
+			msg.ExecutingBinary(e, "error")
 		}
 
 		// out, e := cmd.CombinedOutput()
 		// if e != nil {
-		// 	msg.ExecutingBinary(e, "fatal")
+		// 	msg.ExecutingBinary(e, "error")
 		// }
 
 		_ = cmd.Wait()
 
 		if cmd.ProcessState.ExitCode() != 0 {
-			msg.ExecutingBinary(errors.New("there was an error with PeptideProphet, please check your parameters and input files"), "fatal")
+			msg.ExecutingBinary(errors.New("there was an error with PeptideProphet, please check your parameters and input files"), "error")
 		}
 
 	}
@@ -273,7 +273,7 @@ func refreshParser(p PeptideProphet, file, database, output, temp string) {
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 	_ = cmd.Wait()
 }
@@ -447,7 +447,7 @@ func peptideProphet(p PeptideProphet, params met.PeptideProphet, temp, file stri
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 	_ = cmd.Wait()
 
diff --git a/lib/ext/peptideprophet/peptideprophet_unix.go b/lib/ext/peptideprophet/peptideprophet_unix.go
index 84a39394..d637a598 100644
--- a/lib/ext/peptideprophet/peptideprophet_unix.go
+++ b/lib/ext/peptideprophet/peptideprophet_unix.go
@@ -30,6 +30,6 @@ func (p *PeptideProphet) Deploy(distro string) {
 		unix.UnixPeptideProphetParser(p.UnixPeptideProphetParser)
 		p.DefaultPeptideProphetParser = p.UnixPeptideProphetParser
 	} else {
-		msg.UnsupportedDistribution(errors.New(""), "fatal")
+		msg.UnsupportedDistribution(errors.New(""), "error")
 	}
 }
diff --git a/lib/ext/proteinprophet/deploy_unix.go b/lib/ext/proteinprophet/deploy_unix.go
index 96947169..1d6a532f 100644
--- a/lib/ext/proteinprophet/deploy_unix.go
+++ b/lib/ext/proteinprophet/deploy_unix.go
@@ -29,6 +29,6 @@ func (p *ProteinProphet) Deploy(distro string) {
 		unix.UnixProteinProphet(p.UnixProteinProphet)
 		p.DefaultProteinProphet = p.UnixProteinProphet
 	} else {
-		msg.UnsupportedDistribution(errors.New(""), "fatal")
+		msg.UnsupportedDistribution(errors.New(""), "error")
 	}
 }
diff --git a/lib/ext/proteinprophet/proteinprophet.go b/lib/ext/proteinprophet/proteinprophet.go
index b95bb3d0..e0036a1f 100644
--- a/lib/ext/proteinprophet/proteinprophet.go
+++ b/lib/ext/proteinprophet/proteinprophet.go
@@ -52,7 +52,7 @@ func Run(m met.Data, args []string) met.Data {
 	var pop = New(m.Temp)
 
 	if len(args) < 1 {
-		msg.NoParametersFound(errors.New("missing pep.xml"), "fatal")
+		msg.NoParametersFound(errors.New("missing pep.xml"), "error")
 	}
 
 	// deploy the binaries
@@ -102,12 +102,12 @@ func (p ProteinProphet) Execute(params met.ProteinProphet, home, temp string, ar
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 	_ = cmd.Wait()
 
 	if cmd.ProcessState.ExitCode() != 0 {
-		msg.ExecutingBinary(errors.New("there was an error with ProteinProphet, please check your parameters and input files"), "fatal")
+		msg.ExecutingBinary(errors.New("there was an error with ProteinProphet, please check your parameters and input files"), "error")
 	}
 
 	// copy to work directory
diff --git a/lib/ext/ptmprophet/ptmprophet.go b/lib/ext/ptmprophet/ptmprophet.go
index b4dfc80a..200ebb3e 100644
--- a/lib/ext/ptmprophet/ptmprophet.go
+++ b/lib/ext/ptmprophet/ptmprophet.go
@@ -83,15 +83,10 @@ func (p *PTMProphet) Execute(params met.PTMProphet, args []string) []string {
 
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 	_ = cmd.Wait()
 
-	// if cmd.ProcessState.ExitCode() != 0 {
-	// 	fmt.Println(cmd.Stdout, cmd.Stderr)
-	// 	msg.ExecutingBinary(errors.New("there was an error with PTMProphet, please check your parameters and input files"), "fatal")
-	// }
-
 	// collect all resulting files
 	var customOutput []string
 	if params.KeepOld {
diff --git a/lib/ext/ptmprophet/ptmprophet_unix.go b/lib/ext/ptmprophet/ptmprophet_unix.go
index dd494581..b451b857 100644
--- a/lib/ext/ptmprophet/ptmprophet_unix.go
+++ b/lib/ext/ptmprophet/ptmprophet_unix.go
@@ -21,6 +21,6 @@ func (p *PTMProphet) Deploy(distro string) {
 		unix.UnixPTMProphetParser(p.UnixPTMProphetParser)
 		p.DefaultPTMProphetParser = p.UnixPTMProphetParser
 	} else {
-		msg.UnsupportedDistribution(errors.New(""), "fatal")
+		msg.UnsupportedDistribution(errors.New(""), "error")
 	}
 }
diff --git a/lib/ext/tmtintegrator/tmtintegrator.go b/lib/ext/tmtintegrator/tmtintegrator.go
index 9f13870b..60cd1f9c 100644
--- a/lib/ext/tmtintegrator/tmtintegrator.go
+++ b/lib/ext/tmtintegrator/tmtintegrator.go
@@ -42,7 +42,7 @@ func Run(m met.Data, args []string) met.Data {
 		paramAbs, _ := filepath.Abs(m.TMTIntegrator.Param)
 		binFile, e := ioutil.ReadFile(paramAbs)
 		if e != nil {
-			msg.ReadFile(e, "fatal")
+			msg.ReadFile(e, "error")
 		}
 		m.TMTIntegrator.ParamFile = binFile
 	}
@@ -67,7 +67,7 @@ func (c *TMTIntegrator) Execute(params met.TMTIntegrator, cmdArgs []string) {
 	cmd.Stderr = os.Stderr
 	e := cmd.Start()
 	if e != nil {
-		msg.ExecutingBinary(e, "fatal")
+		msg.ExecutingBinary(e, "error")
 	}
 
 	_ = cmd.Wait()
diff --git a/lib/fas/fas.go b/lib/fas/fas.go
index b166d816..9fde3cb8 100644
--- a/lib/fas/fas.go
+++ b/lib/fas/fas.go
@@ -19,7 +19,7 @@ func ParseFile(filename string) map[string]string {
 
 	f, e := os.Open(filename)
 	if filename == "" || e != nil {
-		msg.ReadFile(errors.New("cannot open the database file"), "error")
+		msg.ReadFile(errors.New("cannot open the database file"), "fatal")
 	}
 	defer f.Close()
 
@@ -84,7 +84,7 @@ func ParseFastaDescription(filename string) map[string][]string {
 
 	f, e := os.Open(filename)
 	if filename == "" || e != nil {
-		msg.ReadFile(errors.New("cannot open FASTA file"), "fatal")
+		msg.ReadFile(errors.New("cannot open FASTA file"), "error")
 	}
 	defer f.Close()
 
diff --git a/lib/fil/fdr.go b/lib/fil/fdr.go
index 1adcfc15..075bfab9 100644
--- a/lib/fil/fdr.go
+++ b/lib/fil/fdr.go
@@ -537,7 +537,7 @@ func ProtXMLFilter(p id.ProtXML, targetFDR, pepProb, protProb float64, isPicked,
 	}
 
 	if currentTopPepProb == 10 {
-		msg.Custom(errors.New("the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter"), "error")
+		msg.Custom(errors.New("the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter"), "fatal")
 	}
 
 	// if the current protein block threshold is below the threshold, we look for the next one
diff --git a/lib/fil/fil.go b/lib/fil/fil.go
index 7a81220b..f0e8790a 100644
--- a/lib/fil/fil.go
+++ b/lib/fil/fil.go
@@ -102,6 +102,7 @@ func Run(f met.Data) met.Data {
 	}
 	var pepxml id.PepXML
 	pepxml.Restore()
+
 	// restoring for the modifications
 	e.Mods = pepxml.Modifications
 	e.AssembleSearchParameters(pepxml.SearchParameters)
@@ -149,7 +150,6 @@ func Run(f met.Data) met.Data {
 
 	// evaluate modifications in data set
 	if f.Filter.Mapmods {
-		//e.UpdateIonModCount()
 		e.UpdatePeptideModCount()
 	}
 
@@ -607,9 +607,6 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 
 			pro.Length = 0
 			pro.PercentCoverage = float32(coverMap[pro.ProteinName])
-			//pro.PctSpectrumIDs = 0.0
-			//pro.GroupProbability = 1.00
-			//pro.Confidence = 1.00
 			pro.HasRazor = true
 
 			if i.Probability > pro.Probability {
@@ -625,9 +622,6 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 			if !ok {
 				pro.Length = 0
 				pro.PercentCoverage = float32(coverMap[pro.ProteinName])
-				//pro.PctSpectrumIDs = 0.0
-				//pro.GroupProbability = 1.00
-				//pro.Confidence = 1.00
 				pro.HasRazor = false
 
 				if i.Probability > pro.Probability {
@@ -645,7 +639,6 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 	//var addedIon = make(map[string]uint8)
 	for _, i := range psm {
 
-		//ionForm := fmt.Sprintf("%s#%d#%.4f", i.Peptide, i.AssumedCharge, i.CalcNeutralPepMass)
 		pro := proteinList[i.Protein]
 		razorProtein, ok := razorMap[i.Peptide]
 
@@ -661,8 +654,7 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 				Weight:             1,
 				GroupWeight:        0,
 				CalcNeutralPepMass: i.CalcNeutralPepMass,
-				//SharedParentProteins: len(i.AlternativeProteins),
-				Razor: 1,
+				Razor:              1,
 			}
 
 			for j := range i.AlternativeProteins {
@@ -670,17 +662,13 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 				pro.IndistinguishableProtein = append(pro.IndistinguishableProtein, j)
 			}
 
-			//pep.NumberOfInstances++
-
 			if i.Probability > pep.InitialProbability {
 				pep.InitialProbability = i.Probability
 			}
 
 			if len(i.AlternativeProteins) < 2 {
-				//pep.IsNondegenerateEvidence = true
 				pep.IsUnique = true
 			} else {
-				//pep.IsNondegenerateEvidence = false
 				pep.IsUnique = false
 			}
 
@@ -689,7 +677,6 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 				pep.Modifications.Index[k] = v
 			}
 
-			//pro.IndistinguishableProtein = i.AlternativeProteins
 			pro.HasRazor = true
 			pro.PeptideIons = append(pro.PeptideIons, pep)
 
@@ -707,23 +694,16 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 				Weight:             0,
 				GroupWeight:        0,
 				CalcNeutralPepMass: i.CalcNeutralPepMass,
-				//SharedParentProteins: len(i.AlternativeProteins),
-				Razor: 0,
+				Razor:              0,
 			}
 
 			if i.Probability > pep.InitialProbability {
 				pep.InitialProbability = i.Probability
 			}
 
-			//pep.PeptideParentProtein = i.AlternativeProteins
-
-			//pep.NumberOfInstances++
-
 			if len(i.AlternativeProteins) < 2 {
-				//pep.IsNondegenerateEvidence = true
 				pep.IsUnique = true
 			} else {
-				//pep.IsNondegenerateEvidence = false
 				pep.IsUnique = false
 			}
 
@@ -732,7 +712,6 @@ func processProteinInferenceIdentifications(psm id.PepIDList, razorMap map[strin
 				pep.Modifications.Index[k] = v
 			}
 
-			//pro.IndistinguishableProtein = i.AlternativeProteins
 			pro.PeptideIons = append(pro.PeptideIons, pep)
 
 			proteinList[i.Protein] = pro
diff --git a/lib/fin/fin.go b/lib/fin/fin.go
index 25f6e42e..af82409a 100644
--- a/lib/fin/fin.go
+++ b/lib/fin/fin.go
@@ -203,7 +203,7 @@ type RunHeader struct {
 	Unknown34         uint32
 }
 
-//SampleInfo contains some other info
+// SampleInfo contains some other info
 type SampleInfo struct {
 	Unknown1        uint32
 	Unknown2        uint32
@@ -307,7 +307,7 @@ type ScanDataPacket struct {
 	Triplets       []float32
 }
 
-//PeakDescriptor is a struct containing more info about the peaks
+// PeakDescriptor is a struct containing more info about the peaks
 type PeakDescriptor struct {
 	Index  uint16
 	Flags  uint8
@@ -511,7 +511,7 @@ func (rd *RawData) ProcessRaw(f string) {
 
 	file, e := os.Open(f)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 
 	// Read headers for file version and RunHeader addresses.
@@ -766,7 +766,7 @@ func (data *RunHeader) Retrieve(rs io.ReadSeeker, info RawFileInfo, ver Version)
 	}
 
 	if data.ScantrailerAddr == 0 {
-		msg.Custom(errors.New(""), "fatal")
+		msg.Custom(errors.New(""), "error")
 	}
 
 }
@@ -776,7 +776,7 @@ func (data *InstID) Retrieve(rs io.ReadSeeker, pos uint64, ver Version) {
 	data.Address = readAt(rs, pos, ver, data)
 }
 
-//// Readers
+// // Readers
 func (data *RunHeader) Read(r io.Reader, v Version) {
 
 	binaryread(r, &data.SampleInfo)
@@ -1238,14 +1238,14 @@ func readAt(rs io.ReadSeeker, pos uint64, v Version, data reader) uint64 {
 
 	_, e1 := rs.Seek(int64(pos), 0)
 	if e1 != nil {
-		msg.Custom(errors.New("error seeking file"), "fatal")
+		msg.Custom(errors.New("error seeking file"), "error")
 	}
 
 	data.Read(rs, v)
 
 	spos, e2 := rs.Seek(0, 1)
 	if e2 != nil {
-		msg.Custom(errors.New("error determining position in file"), "fatal")
+		msg.Custom(errors.New("error determining position in file"), "error")
 	}
 
 	return uint64(spos)
@@ -1257,7 +1257,7 @@ func readBetween(rs io.ReadSeeker, begin uint64, end uint64, v Version, data rea
 
 	_, e := rs.Seek(int64(begin), 0)
 	if e != nil {
-		msg.Custom(errors.New("error seeking file"), "fatal")
+		msg.Custom(errors.New("error seeking file"), "error")
 	}
 
 	// may fail because of memory requirements
diff --git a/lib/gth/gth.go b/lib/gth/gth.go
index 669ed8cc..8415f298 100644
--- a/lib/gth/gth.go
+++ b/lib/gth/gth.go
@@ -39,7 +39,7 @@ func UpdateChecker(v, b string) {
 
 		body, e := ioutil.ReadAll(res.Body)
 		if e != nil {
-			msg.Custom(e, "fatal")
+			msg.Custom(e, "error")
 		}
 
 		var rel Releases
@@ -50,23 +50,16 @@ func UpdateChecker(v, b string) {
 
 		} else {
 
-			local := strings.Split(v, ".")
-			local[0] = strings.Replace(local[0], "v", "", 1)
+			local := strings.Replace(v, ".", "", -1)
+			local = strings.Replace(local, "v", "", 1)
 
-			remote := strings.Split(rel[0].TagName, ".")
-			remote[0] = strings.Replace(remote[0], "v", "", 1)
+			remote := strings.Replace(rel[0].TagName, ".", "", -1)
+			remote = strings.Replace(remote, "v", "", 1)
 
-			outdatedMajorVersion := remote[0] > local[0]
-			//outdatedMinorVersion := (remote[0] == local[0]) && (remote[1] > local[1])
-			//outdated := outdatedMajorVersion || outdatedMinorVersion
-
-			outdated := outdatedMajorVersion
-
-			if outdated {
+			if remote > local {
 				logrus.Warning("There is a new version of Philosopher available for download: https://github.com/Nesvilab/philosopher/releases")
 			}
 
 		}
 	}
-
 }
diff --git a/lib/id/pep.go b/lib/id/pep.go
index bb456b01..b8f5efa2 100644
--- a/lib/id/pep.go
+++ b/lib/id/pep.go
@@ -213,13 +213,11 @@ func (p *PepXML) Read(f string) {
 			_, ok := p.Modifications.Index[key]
 			if !ok {
 				m := mod.Modification{
-					Index: key,
-					Type:  mod.Assigned,
-					//MonoIsotopicMass: i.Mass,
+					Index:     key,
+					Type:      mod.Assigned,
 					MassDiff:  uti.ToFixed(i.MassDiff, 4),
 					Variable:  variable,
 					AminoAcid: string(i.AminoAcid),
-					//IsobaricMods: make(map[string]float64),
 				}
 
 				p.Modifications.Index[key] = m
@@ -239,15 +237,11 @@ func (p *PepXML) Read(f string) {
 			if !ok {
 
 				m := mod.Modification{
-					Index: key,
-					Type:  mod.Assigned,
-					//MonoIsotopicMass:  i.Mass,
+					Index:     key,
+					Type:      mod.Assigned,
 					MassDiff:  uti.ToFixed(i.MassDiff, 4),
 					Variable:  variable,
 					AminoAcid: fmt.Sprintf("%s-term", i.Terminus),
-					//IsProteinTerminus: string(i.ProteinTerminus),
-					//Terminus:          strings.ToLower(string(i.Terminus)),
-					//IsobaricMods: make(map[string]float64),
 				}
 
 				p.Modifications.Index[key] = m
@@ -299,7 +293,7 @@ func ReadPepXMLInput(xmlFile, decoyTag, temp string, models bool) (PepIDListPtrs
 		list := uti.IOReadDir(xmlFile, "pep.xml")
 
 		if len(list) == 0 {
-			msg.NoParametersFound(errors.New("missing PeptideProphet pepXML files"), "fatal")
+			msg.NoParametersFound(errors.New("missing PeptideProphet pepXML files"), "error")
 		}
 
 		// in case both PeptideProphet and PTMProphet files are present, use
@@ -438,12 +432,6 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 
 				psm.Probability = j.PeptideProphetResult.Probability
 
-				// for _, k := range j.PeptideProphetResult.SearchScoreSummary.Parameter {
-
-				// 	if k.Name == "massd" {
-				// 		//psm.IsoMassD, _ = strconv.Atoi(k.Value)
-				// 	}
-				// }
 			}
 
 			if string(j.Analysis) == "interprophet" {
@@ -475,12 +463,6 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 			} else if string(j.Name) == "deltacn" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.DeltaCN = value
-			} else if string(j.Name) == "deltacnstar" {
-				//value, _ := strconv.ParseFloat(j.Value, 64)
-				//psm.DeltaCNStar = value
-			} else if string(j.Name) == "spscore" {
-				//value, _ := strconv.ParseFloat(j.Value, 64)
-				//psm.SPScore = value
 			} else if string(j.Name) == "sprank" {
 				value, _ := strconv.ParseFloat(j.Value, 64)
 				psm.SPRank = value
@@ -614,27 +596,6 @@ func (p *PeptideIdentification) mapModsFromPepXML(m spc.ModificationInfo, mods m
 	}
 }
 
-// getMassDeviation calculates the mass deviation for a pepXML file based on the 0 mass difference
-// func getMassDeviation(sq []spc.SpectrumQuery) float64 {
-
-// 	var countZero int
-// 	var massZero float64
-// 	var adjustedMass float64
-
-// 	for _, i := range sq {
-// 		for _, j := range i.SearchResult.SearchHit {
-// 			if math.Abs(j.Massdiff) >= -0.1 && math.Abs(j.Massdiff) <= 0.1 {
-// 				countZero++
-// 				massZero += j.Massdiff
-// 			}
-// 		}
-// 	}
-
-// 	adjustedMass = massZero / float64(countZero)
-
-// 	return adjustedMass
-// }
-
 // PromoteProteinIDs changes the identification in cases where the reference protein is a decoy and
 // the alternative proteins contains target proteins.
 func (p *PepXML4Serialiazation) PromoteProteinIDs() {
@@ -854,7 +815,7 @@ func (p *PepIDList) Serialize(level string) {
 	} else if level == "ion" {
 		dest = sys.IonBin()
 	} else {
-		msg.Custom(errors.New("cannot determine binary data class"), "fatal")
+		msg.Custom(errors.New("cannot determine binary data class"), "error")
 	}
 	sys.Serialize(p, dest)
 }
@@ -871,7 +832,7 @@ func (p *PepIDListPtrs) Serialize(level string) {
 	} else if level == "ion" {
 		dest = sys.IonBin()
 	} else {
-		msg.Custom(errors.New("cannot determine binary data class"), "fatal")
+		msg.Custom(errors.New("cannot determine binary data class"), "error")
 	}
 	sys.Serialize(p, dest)
 }
@@ -888,7 +849,7 @@ func (p *PepIDList) Restore(level string) {
 	} else if level == "ion" {
 		dest = sys.IonBin()
 	} else {
-		msg.Custom(errors.New("cannot determine binary data class"), "fatal")
+		msg.Custom(errors.New("cannot determine binary data class"), "error")
 	}
 	sys.Restore(p, dest, false)
 }
diff --git a/lib/id/pro.go b/lib/id/pro.go
index c10ff9ed..d08ee56b 100644
--- a/lib/id/pro.go
+++ b/lib/id/pro.go
@@ -109,7 +109,7 @@ func (p ProtIDList) Swap(i, j int) {
 	p[i], p[j] = p[j], p[i]
 }
 
-// Read ...
+// Read is the mmain function to read prot.xml files
 func (p *ProtXML) Read(f string) {
 
 	var xml spc.ProtXML
@@ -213,7 +213,7 @@ func (p *ProtXML) Read(f string) {
 	p.Groups = groups
 
 	if len(groups) == 0 {
-		msg.NoProteinFound(errors.New(""), "fatal")
+		msg.NoProteinFound(errors.New(""), "error")
 	}
 
 }
diff --git a/lib/met/met.go b/lib/met/met.go
index 1523f724..b198a054 100644
--- a/lib/met/met.go
+++ b/lib/met/met.go
@@ -480,7 +480,7 @@ func CleanTemp(dir string) {
 
 	e := os.RemoveAll(dir)
 	if e != nil {
-		msg.Custom(e, "error")
+		msg.Custom(e, "fatal")
 	}
 }
 
@@ -489,12 +489,12 @@ func (d *Data) Serialize() {
 
 	b, e := msgpack.Marshal(&d)
 	if e != nil {
-		msg.MarshalFile(e, "fatal")
+		msg.MarshalFile(e, "error")
 	}
 
 	e = ioutil.WriteFile(sys.Meta(), b, sys.FilePermission())
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 
 }
@@ -524,7 +524,7 @@ func (d *Data) Restore(f string) {
 func (d Data) FunctionInitCheckUp() {
 
 	if len(d.UUID) < 1 && len(d.Home) < 1 {
-		msg.WorkspaceNotFound(errors.New("failed to checkup the initialization"), "fatal")
+		msg.WorkspaceNotFound(errors.New("failed to checkup the initialization"), "error")
 	}
 
 	if _, e := os.Stat(d.Temp); os.IsNotExist(e) && len(d.UUID) > 0 {
diff --git a/lib/mod/mod.go b/lib/mod/mod.go
index d4b0c2a2..60f895ea 100644
--- a/lib/mod/mod.go
+++ b/lib/mod/mod.go
@@ -24,10 +24,6 @@ type Modification struct {
 	Position     int
 	Type         ModTypeType
 	Variable     bool
-	//IsProteinTerminus string
-	//Terminus          string
-	//MonoIsotopicMass  float64
-	//AverageMass       float64
 }
 
 // Modifications is a collection of modifications
@@ -52,31 +48,3 @@ func (m ModificationsSlice) ToMap() Modifications {
 	}
 	return Modifications{Index: Index}
 }
-
-// Serialize saves to disk a msgpack version of the Isobaric data structure
-// func (m *Modifications) Serialize() {
-
-// 	b, e := msgpack.Marshal(&m)
-// 	if e != nil {
-// 		msg.MarshalFile(e, "fatal")
-// 	}
-
-// 	e = ioutil.WriteFile(sys.EvModificationsBin(), b, sys.FilePermission())
-// 	if e != nil {
-// 		msg.SerializeFile(e, "fatal")
-// 	}
-// }
-
-// Restore reads philosopher results files and restore the data sctructure
-// func (m *Modifications) Restore() {
-
-// 	b, e := ioutil.ReadFile(sys.EvModificationsBin())
-// 	if e != nil {
-// 		msg.MarshalFile(e, "warning")
-// 	}
-
-// 	e = msgpack.Unmarshal(b, &m)
-// 	if e != nil {
-// 		msg.SerializeFile(e, "warning")
-// 	}
-// }
diff --git a/lib/msg/msg.go b/lib/msg/msg.go
index 25c9fef7..1aa3f8d2 100644
--- a/lib/msg/msg.go
+++ b/lib/msg/msg.go
@@ -312,10 +312,10 @@ func callLogrus(m, t string) {
 		logrus.Info(m)
 	case "warning":
 		logrus.Warning(m)
-	case "error":
-		logrus.Error(m)
 	case "fatal":
 		logrus.Error(m)
+	case "error":
+		logrus.Error(m)
 		panic(m)
 	default:
 		logrus.Error(m)
diff --git a/lib/mzn/mzn.go b/lib/mzn/mzn.go
index a4415d60..76ff300f 100644
--- a/lib/mzn/mzn.go
+++ b/lib/mzn/mzn.go
@@ -125,7 +125,7 @@ func (p *MsData) ReadRaw(fileName, f string) {
 
 			siVal1, e := strconv.ParseFloat(parts[5], 64)
 			if e != nil {
-				msg.CastFloatToString(e, "fatal")
+				msg.CastFloatToString(e, "error")
 			} else {
 				spec.Precursor.SelectedIon = siVal1
 				spec.Precursor.TargetIon = siVal1
@@ -133,7 +133,7 @@ func (p *MsData) ReadRaw(fileName, f string) {
 
 			siVal2, e := strconv.ParseFloat(parts[6], 64)
 			if e != nil {
-				msg.CastFloatToString(e, "fatal")
+				msg.CastFloatToString(e, "error")
 			} else {
 				//spec.Precursor.SelectedIonIntensity = siVal2
 				spec.Precursor.TargetIonIntensity = siVal2
@@ -181,7 +181,7 @@ func (p *MsData) ReadRaw(fileName, f string) {
 	}
 
 	if len(spectra) == 0 {
-		msg.NoSpectraFound(errors.New(""), "fatal")
+		msg.NoSpectraFound(errors.New(""), "error")
 	}
 
 	p.Spectra = spectra
@@ -213,7 +213,7 @@ func (p *MsData) Read(f string) {
 	}
 
 	if len(spectra) == 0 {
-		msg.NoSpectraFound(errors.New(""), "fatal")
+		msg.NoSpectraFound(errors.New(""), "error")
 	}
 
 	p.Spectra = spectra
@@ -245,7 +245,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 		if string(j.Accession) == "MS:1000016" {
 			val, e := strconv.ParseFloat(j.Value, 64)
 			if e != nil {
-				msg.CastFloatToString(e, "error")
+				msg.CastFloatToString(e, "fatal")
 			}
 			spec.ScanStartTime = val
 		}
@@ -270,7 +270,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000827" {
 				val, e := strconv.ParseFloat(j.Value, 64)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.TargetIon = val
 			}
@@ -278,7 +278,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000828" {
 				val, e := strconv.ParseFloat(j.Value, 64)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.IsolationWindowLowerOffset = val
 			}
@@ -286,7 +286,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000829" {
 				val, e := strconv.ParseFloat(j.Value, 64)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.IsolationWindowUpperOffset = val
 			}
@@ -297,7 +297,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000744" {
 				val, e := strconv.ParseFloat(j.Value, 64)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.SelectedIon = val
 			}
@@ -305,7 +305,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000041" {
 				val, e := strconv.Atoi(j.Value)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.ChargeState = val
 			}
@@ -313,7 +313,7 @@ func processSpectrum(mzSpec psi.Spectrum) Spectrum {
 			if string(j.Accession) == "MS:1000042" {
 				val, e := strconv.ParseFloat(j.Value, 64)
 				if e != nil {
-					msg.CastFloatToString(e, "fatal")
+					msg.CastFloatToString(e, "error")
 				}
 				spec.Precursor.SelectedIonIntensity = val
 			}
@@ -401,7 +401,7 @@ func readEncoded(bin []byte, precision, isCompressed string) []float64 {
 	if isCompressed == "1" {
 		r, e := zlib.NewReader(b64)
 		if e != nil {
-			msg.ReadingMzMLZlib(e, "error")
+			msg.ReadingMzMLZlib(e, "fatal")
 			var emptyArray []float64
 			emptyArray = append(emptyArray, 0.0)
 			return emptyArray
diff --git a/lib/obo/obo.go b/lib/obo/obo.go
index 8018cd36..04abca29 100644
--- a/lib/obo/obo.go
+++ b/lib/obo/obo.go
@@ -93,7 +93,7 @@ func (m *Onto) Parse() {
 
 	file, e := os.Open(m.OboFile)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	defer file.Close()
 
diff --git a/lib/pip/pip.go b/lib/pip/pip.go
index f703fc20..d5e8e3d7 100644
--- a/lib/pip/pip.go
+++ b/lib/pip/pip.go
@@ -83,12 +83,12 @@ func DeployParameterFile(temp string) string {
 
 	param, e := Asset("philosopher.yml")
 	if e != nil {
-		msg.DeployAsset(errors.New("pipeline configuration file"), "fatal")
+		msg.DeployAsset(errors.New("pipeline configuration file"), "error")
 	}
 
 	e = ioutil.WriteFile(file, param, sys.FilePermission())
 	if e != nil {
-		msg.DeployAsset(errors.New("pipeline configuration file"), "fatal")
+		msg.DeployAsset(errors.New("pipeline configuration file"), "error")
 	}
 
 	return file
@@ -145,7 +145,6 @@ func AnnotateDatabase(meta met.Data, p Directives, dir string, data []string) me
 	os.Chdir(dir)
 
 	for i := 1; i < len(data); i++ {
-		//source := fmt.Sprintf("%s%s.meta%sdb.bin", data[0], string(filepath.Separator), string(filepath.Separator))
 		destination := fmt.Sprintf("%s%s.meta%sdb.bin", data[i], string(filepath.Separator), string(filepath.Separator))
 
 		// Read all content of src to data
@@ -159,7 +158,6 @@ func AnnotateDatabase(meta met.Data, p Directives, dir string, data []string) me
 			log.Fatal(e)
 		}
 
-		//meta.Serialize()
 	}
 
 	met.CleanTemp(meta.Temp)
@@ -172,10 +170,6 @@ func DBSearch(meta met.Data, p Directives, dir string, data []string) met.Data {
 
 	logrus.Info("Running the Database Search")
 
-	// if meta.Pipeline.Verbose == true {
-	// 	p.DatabaseSearch.MSFragger.ToCmdString()
-	// }
-
 	// reload the meta data
 	meta.Restore(sys.Meta())
 
@@ -193,7 +187,7 @@ func DBSearch(meta met.Data, p Directives, dir string, data []string) met.Data {
 			gobExtC := fmt.Sprintf("*.%s", p.DatabaseSearch.Comet.RawExtension)
 			filesC, e := filepath.Glob(gobExtC)
 			if e != nil {
-				msg.Custom(e, "fatal")
+				msg.Custom(e, "error")
 			}
 
 			if len(filesC) > 0 {
@@ -226,7 +220,7 @@ func DBSearch(meta met.Data, p Directives, dir string, data []string) met.Data {
 			gobExtM := fmt.Sprintf("*.%s", p.DatabaseSearch.MSFragger.Extension)
 			filesM, e := filepath.Glob(gobExtM)
 			if e != nil {
-				msg.Custom(e, "fatal")
+				msg.Custom(e, "error")
 			}
 
 			if len(filesM) > 0 {
@@ -278,7 +272,7 @@ func PeptideProphet(meta met.Data, p Directives, dir string, data []string) met.
 				gobExt := fmt.Sprintf("*.%s", p.PeptideProphet.FileExtension)
 				files, e := filepath.Glob(gobExt)
 				if e != nil {
-					msg.Custom(e, "fatal")
+					msg.Custom(e, "error")
 				}
 
 				peptideprophet.Run(meta, files)
@@ -326,7 +320,7 @@ func PeptideProphet(meta met.Data, p Directives, dir string, data []string) met.
 
 			files, e := filepath.Glob(gobExt)
 			if e != nil {
-				msg.Custom(e, "fatal")
+				msg.Custom(e, "error")
 			}
 
 			peptideprophet.Run(meta, files)
@@ -521,9 +515,6 @@ func CombinedProteinList(meta met.Data, p Directives, dir string, data []string)
 
 	if _, err := os.Stat(path.Dir(proBin)); err == nil {
 		os.RemoveAll(path.Dir(proBin))
-		// if e != nil {
-		// 	log.Fatal(e)
-		// }
 	}
 
 	return meta
diff --git a/lib/psi/psi.go b/lib/psi/psi.go
index b91d1ae3..e91d6a04 100644
--- a/lib/psi/psi.go
+++ b/lib/psi/psi.go
@@ -100,7 +100,7 @@ func (p *IndexedMzML) Parse(f string) {
 
 	xmlFile, e := os.Open(f)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	defer xmlFile.Close()
 	b, _ := ioutil.ReadAll(xmlFile)
@@ -112,7 +112,7 @@ func (p *IndexedMzML) Parse(f string) {
 	decoder.CharsetReader = charset.NewReader
 
 	if e = decoder.Decode(&mzml); e != nil {
-		msg.DecodeMsgPck(e, "fatal")
+		msg.DecodeMsgPck(e, "error")
 	}
 
 	p.MzML = mzml.MzML
@@ -125,7 +125,7 @@ func (p *MzIdentML) Parse(f string) {
 
 	xmlFile, e := os.Open(f)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 
 	defer xmlFile.Close()
@@ -148,7 +148,7 @@ func (p *MzIdentML) Write() {
 
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer file.Close()
 
diff --git a/lib/qua/bqt.go b/lib/qua/bqt.go
index bc988200..e659b150 100644
--- a/lib/qua/bqt.go
+++ b/lib/qua/bqt.go
@@ -74,18 +74,18 @@ func parseClusterFile(cls, database string) List {
 
 	f, e := os.Open(cls)
 	if e != nil {
-		msg.Custom(errors.New("cannot open cluster file"), "fatal")
+		msg.Custom(errors.New("cannot open cluster file"), "error")
 	}
 	defer f.Close()
 
 	reheader, e1 := regexp.Compile(`^>Cluster\s+(.*)`)
 	if e1 != nil {
-		msg.Custom(errors.New("cannot compile Cluster header regex"), "fatal")
+		msg.Custom(errors.New("cannot compile Cluster header regex"), "error")
 	}
 
 	reseq, e2 := regexp.Compile(`\|(.*)\|.*`)
 	if e2 != nil {
-		msg.Custom(errors.New("cannot compile Cluster description regex"), "fatal")
+		msg.Custom(errors.New("cannot compile Cluster description regex"), "error")
 	}
 
 	scanner := bufio.NewScanner(f)
@@ -98,7 +98,7 @@ func parseClusterFile(cls, database string) List {
 			num := cluster[1]
 			i, e := strconv.Atoi(num)
 			if e != nil {
-				msg.Custom(errors.New("FASTA header not found"), "fatal")
+				msg.Custom(errors.New("FASTA header not found"), "error")
 			}
 			clusterNumber = i
 
@@ -111,7 +111,7 @@ func parseClusterFile(cls, database string) List {
 				centroid := strings.Split(scanner.Text(), "|")
 				//centroid := reseq.FindStringSubmatch(scanner.Text())
 				if len(centroid) < 2 {
-					msg.Custom(errors.New("FASTA file contains non-formatted sequence headers"), "fatal")
+					msg.Custom(errors.New("FASTA file contains non-formatted sequence headers"), "error")
 				}
 				centroidmap[clusterNumber] = centroid[1]
 
@@ -262,28 +262,28 @@ func getFile(getAll bool, resultDir string, organism string) (faMap map[string][
 	// tries to create an output file
 	output, e := os.Create(outfile)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer output.Close()
 
 	// Tries to query data from Uniprot
 	response, e := http.Get(query)
 	if e != nil {
-		msg.Custom(errors.New("could not find the annotation file"), "fatal")
+		msg.Custom(errors.New("could not find the annotation file"), "error")
 	}
 	defer response.Body.Close()
 
 	// Tries to download data from Uniprot
 	_, e = io.Copy(output, response.Body)
 	if e != nil {
-		msg.Custom(errors.New("cannot download the annotation file"), "fatal")
+		msg.Custom(errors.New("cannot download the annotation file"), "error")
 	}
 
 	faMap = make(map[string][]string)
 
 	f, e := os.Open(outfile)
 	if outfile == "" || e != nil {
-		msg.Custom(errors.New("emty or inexisting file"), "fatal")
+		msg.Custom(errors.New("emty or inexisting file"), "error")
 	}
 	defer f.Close()
 
@@ -305,7 +305,7 @@ func savetoDisk(list List, temp, uid string) {
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer file.Close()
 
@@ -351,7 +351,7 @@ func savetoDisk(list List, temp, uid string) {
 
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	var faMap = make(map[string][]string)
@@ -420,7 +420,7 @@ func savetoDisk(list List, temp, uid string) {
 
 			_, e := io.WriteString(file, line)
 			if e != nil {
-				msg.WriteToFile(e, "fatal")
+				msg.WriteToFile(e, "error")
 			}
 		}
 
diff --git a/lib/qua/lfq.go b/lib/qua/lfq.go
index f2c797eb..375dd8b8 100644
--- a/lib/qua/lfq.go
+++ b/lib/qua/lfq.go
@@ -226,7 +226,7 @@ func calculateIntensities(e rep.Evidence) rep.Evidence {
 	logrus.Info("Assigning intensities to data layers")
 
 	if len(e.PSM) < 1 || len(e.Ions) < 1 {
-		msg.QuantifyingData(errors.New("the PSM list is enpty"), "fatal")
+		msg.QuantifyingData(errors.New("the PSM list is enpty"), "error")
 	}
 
 	var peptideIntMap = make(map[string]float64)
diff --git a/lib/qua/qua.go b/lib/qua/qua.go
index b718f2b1..bc661846 100644
--- a/lib/qua/qua.go
+++ b/lib/qua/qua.go
@@ -60,7 +60,7 @@ func RunIsobaricLabelQuantification(p met.Quantify, mods bool) met.Quantify {
 	var sourceList []string
 
 	if p.Brand == "" {
-		msg.NoParametersFound(errors.New("you need to specify a brand type (tmt or itraq)"), "fatal")
+		msg.NoParametersFound(errors.New("you need to specify a brand type (tmt or itraq)"), "error")
 	}
 
 	var evi rep.Evidence
@@ -637,7 +637,7 @@ func classification(evi rep.Evidence, mods, best bool, remove, purity, probabili
 	}
 
 	if remove != 0 && !quantCheckUp {
-		msg.NoParametersFound(errors.New("no reporter ions found. Check your MS level, or update msconvert"), "fatal")
+		msg.NoParametersFound(errors.New("no reporter ions found. Check your MS level, or update msconvert"), "error")
 	}
 
 	// 2nd check: best PSM
diff --git a/lib/qua/spc.go b/lib/qua/spc.go
index 12171c28..ff61031d 100644
--- a/lib/qua/spc.go
+++ b/lib/qua/spc.go
@@ -64,50 +64,3 @@ func CalculateSpectralCounts(e rep.Evidence) rep.Evidence {
 
 	return e
 }
-
-// func CalculateSpectralCounts(e rep.Evidence) rep.Evidence {
-
-// 	var uniqueIonPSM = make(map[string]string)
-// 	var razorIonPSM = make(map[string]string)
-
-// 	var sequences = make(map[string]int)
-
-// 	for _, i := range e.PSM {
-
-// 		sequences[i.Peptide]++
-
-// 		if i.IsUnique {
-// 			uniqueIonPSM[i.SpectrumFileName()] = i.ProteinID
-// 		}
-// 		if i.IsURazor {
-// 			razorIonPSM[i.SpectrumFileName()] = i.ProteinID
-// 		}
-// 	}
-
-// 	for i := range e.Peptides {
-// 		v, ok := sequences[e.Peptides[i].Sequence]
-// 		if ok {
-// 			e.Peptides[i].Spc += v
-// 		}
-// 	}
-
-// 	for i := range e.Proteins {
-
-// 		for _, j := range e.Proteins[i].TotalPeptideIons {
-
-// 			e.Proteins[i].TotalSpC += len(j.Spectra)
-
-// 			if j.IsUnique {
-// 				e.Proteins[i].UniqueSpC += len(j.Spectra)
-// 			}
-
-// 			if j.IsURazor {
-// 				e.Proteins[i].URazorSpC += len(j.Spectra)
-// 			}
-
-// 		}
-
-// 	}
-
-// 	return e
-// }
diff --git a/lib/rep/ion.go b/lib/rep/ion.go
index 0f3db31f..cdb5d57e 100644
--- a/lib/rep/ion.go
+++ b/lib/rep/ion.go
@@ -118,7 +118,7 @@ func (evi IonEvidenceList) IonReport(workspace, brand, decoyTag string, channels
 	file, e := os.Create(output)
 	bw := bufio.NewWriter(file)
 	if e != nil {
-		msg.WriteFile(errors.New("peptide ion output file"), "fatal")
+		msg.WriteFile(errors.New("peptide ion output file"), "error")
 	}
 	defer file.Close()
 	defer bw.Flush()
@@ -292,7 +292,7 @@ func (evi IonEvidenceList) IonReport(workspace, brand, decoyTag string, channels
 
 	_, e = io.WriteString(bw, header)
 	if e != nil {
-		msg.WriteToFile(errors.New("cannot print Ion to file"), "fatal")
+		msg.WriteToFile(errors.New("cannot print Ion to file"), "error")
 	}
 
 	for _, i := range printSet {
@@ -487,7 +487,7 @@ func (evi IonEvidenceList) IonReport(workspace, brand, decoyTag string, channels
 
 		_, e = io.WriteString(bw, line)
 		if e != nil {
-			msg.WriteToFile(errors.New("cannot print Ions to file"), "fatal")
+			msg.WriteToFile(errors.New("cannot print Ions to file"), "error")
 		}
 	}
 
diff --git a/lib/rep/modification.go b/lib/rep/modification.go
index 5d5cd300..1be7c0b3 100644
--- a/lib/rep/modification.go
+++ b/lib/rep/modification.go
@@ -214,7 +214,7 @@ func (evi *Evidence) ModificationReport(workspace string, hasPrefix bool) {
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("could not create report files"), "error")
+		msg.WriteFile(errors.New("could not create report files"), "fatal")
 	}
 	defer file.Close()
 
@@ -222,7 +222,7 @@ func (evi *Evidence) ModificationReport(workspace string, hasPrefix bool) {
 
 	_, e = io.WriteString(file, line)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range evi.Modifications.MassBins {
@@ -236,7 +236,7 @@ func (evi *Evidence) ModificationReport(workspace string, hasPrefix bool) {
 		line += "\n"
 		_, e = io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
@@ -249,7 +249,7 @@ func (evi *Evidence) PlotMassHist() {
 
 	file, e := os.Create(outfile)
 	if e != nil {
-		msg.WriteFile(errors.New("could not create output for delta mass binning"), "fatal")
+		msg.WriteFile(errors.New("could not create output for delta mass binning"), "error")
 	}
 	defer file.Close()
 
@@ -297,7 +297,7 @@ func (evi *Evidence) PlotMassHist() {
 	io.WriteString(file, "</body>")
 
 	if e != nil {
-		msg.Custom(errors.New("there was an error trying to plot the mass distribution"), "fatal")
+		msg.Custom(errors.New("there was an error trying to plot the mass distribution"), "error")
 	}
 
 	// copy to work directory
diff --git a/lib/rep/msstats.go b/lib/rep/msstats.go
index 9eab7f20..7e3c48d2 100644
--- a/lib/rep/msstats.go
+++ b/lib/rep/msstats.go
@@ -32,7 +32,7 @@ func (evi Evidence) MetaMSstatsReport(workspace, brand string, channels int, has
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create MSstats report"), "error")
+		msg.WriteFile(errors.New("cannot create MSstats report"), "fatal")
 	}
 	defer file.Close()
 
@@ -82,7 +82,7 @@ func (evi Evidence) MetaMSstatsReport(workspace, brand string, channels int, has
 
 	_, e = io.WriteString(file, header)
 	if e != nil {
-		msg.WriteToFile(errors.New("cannot print PSM to file"), "fatal")
+		msg.WriteToFile(errors.New("cannot print PSM to file"), "error")
 	}
 
 	for _, i := range printSet {
@@ -252,7 +252,7 @@ func (evi Evidence) MetaMSstatsReport(workspace, brand string, channels int, has
 
 		_, e = io.WriteString(file, line)
 		if e != nil {
-			msg.WriteToFile(errors.New("cannot write to MSstats report"), "fatal")
+			msg.WriteToFile(errors.New("cannot write to MSstats report"), "error")
 		}
 	}
 }
diff --git a/lib/rep/peptide.go b/lib/rep/peptide.go
index e97a9b3e..c1471db6 100644
--- a/lib/rep/peptide.go
+++ b/lib/rep/peptide.go
@@ -147,7 +147,7 @@ func (evi PeptideEvidenceList) PeptideReport(workspace, brand, decoyTag string,
 	file, e := os.Create(output)
 	bw := bufio.NewWriter(file)
 	if e != nil {
-		msg.WriteFile(errors.New("peptide output file"), "fatal")
+		msg.WriteFile(errors.New("peptide output file"), "error")
 	}
 	defer file.Close()
 	defer bw.Flush()
@@ -319,7 +319,7 @@ func (evi PeptideEvidenceList) PeptideReport(workspace, brand, decoyTag string,
 	//_, e = io.WriteString(file, header)
 	_, e = io.WriteString(bw, header)
 	if e != nil {
-		msg.WriteToFile(errors.New("cannot print PSM to file"), "fatal")
+		msg.WriteToFile(errors.New("cannot print PSM to file"), "error")
 	}
 
 	for _, i := range printSet {
@@ -516,7 +516,7 @@ func (evi PeptideEvidenceList) PeptideReport(workspace, brand, decoyTag string,
 
 		_, e = io.WriteString(bw, line)
 		if e != nil {
-			msg.WriteToFile(errors.New("cannot print Peptides to file"), "fatal")
+			msg.WriteToFile(errors.New("cannot print Peptides to file"), "error")
 		}
 	}
 }
diff --git a/lib/rep/protein.go b/lib/rep/protein.go
index bd39b84c..d0d2858b 100644
--- a/lib/rep/protein.go
+++ b/lib/rep/protein.go
@@ -174,7 +174,7 @@ func (evi *Evidence) AssembleProteinReport(pro id.ProtIDList, weight float64, de
 	dtb.Restore()
 
 	if len(dtb.Records) < 1 {
-		msg.DatabaseNotFound(errors.New(""), "fatal")
+		msg.DatabaseNotFound(errors.New(""), "error")
 	}
 
 	// fix the name sand headers and pull database information into protein report
@@ -257,7 +257,7 @@ func (eviProteins ProteinEvidenceList) ProteinReport(workspace, brand, decoyTag
 	file, e := os.Create(output)
 	bw := bufio.NewWriter(file)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create protein report"), "error")
+		msg.WriteFile(errors.New("cannot create protein report"), "fatal")
 	}
 	defer file.Close()
 	defer bw.Flush()
@@ -427,7 +427,7 @@ func (eviProteins ProteinEvidenceList) ProteinReport(workspace, brand, decoyTag
 
 	_, e = io.WriteString(bw, header)
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	for _, i := range printSet {
@@ -664,7 +664,7 @@ func (eviProteins ProteinEvidenceList) ProteinReport(workspace, brand, decoyTag
 
 		_, e = io.WriteString(bw, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 
 	}
@@ -678,7 +678,7 @@ func (eviProteins ProteinEvidenceList) ProteinFastaReport(workspace string, hasD
 	file, e := os.Create(output)
 	bw := bufio.NewWriter(file)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer file.Close()
 	defer bw.Flush()
@@ -699,7 +699,7 @@ func (eviProteins ProteinEvidenceList) ProteinFastaReport(workspace string, hasD
 		line := ">" + header + "\n" + i.Sequence + "\n"
 		_, e = io.WriteString(bw, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 	}
 }
diff --git a/lib/rep/psm.go b/lib/rep/psm.go
index 38c3c0b0..f1560b97 100644
--- a/lib/rep/psm.go
+++ b/lib/rep/psm.go
@@ -72,7 +72,7 @@ func (evi *Evidence) AssemblePSMReport(pep id.PepIDList, decoyTag string) {
 		p.IonMobility = i.IonMobility
 		p.CompensationVoltage = i.CompensationVoltage
 		p.MappedGenes = make(map[string]struct{})
-		p.MappedProteins = make(map[string]int)
+		p.MappedProteins = make(map[string]string)
 		p.Modifications = i.Modifications
 		p.MSFraggerLoc = i.MSFragerLoc
 		if i.UncalibratedPrecursorNeutralMass > 0 {
@@ -88,9 +88,9 @@ func (evi *Evidence) AssemblePSMReport(pep id.PepIDList, decoyTag string) {
 			p.ModifiedPeptide = ""
 		}
 
-		for j := range i.AlternativeProteins {
+		for j, k := range i.AlternativeProteins {
 			if !strings.Contains(j, decoyTag) {
-				p.MappedProteins[j]++
+				p.MappedProteins[j] = k
 			}
 		}
 
@@ -159,7 +159,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	file, e := os.Create(output)
 	bw := bufio.NewWriter(file)
 	if e != nil {
-		msg.WriteFile(errors.New("cannot create report file, "+e.Error()), "fatal")
+		msg.WriteFile(errors.New("cannot create report file, "+e.Error()), "error")
 	}
 	defer file.Close()
 	defer bw.Flush()
@@ -424,7 +424,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 
 	_, e = io.WriteString(bw, header)
 	if e != nil {
-		msg.WriteToFile(errors.New("cannot print PSM to file"), "fatal")
+		msg.WriteToFile(errors.New("cannot print PSM to file"), "error")
 	}
 
 	for _, i := range printSet {
@@ -726,7 +726,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 
 		_, e = io.WriteString(bw, line)
 		if e != nil {
-			msg.WriteToFile(e, "fatal")
+			msg.WriteToFile(e, "error")
 		}
 	}
 }
@@ -739,13 +739,13 @@ func (evi *Evidence) PSMLocalizationReport(workspace, decoyTag string, hasRazor,
 	// create result file
 	file, e := os.Create(output)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer file.Close()
 
 	_, e = io.WriteString(file, "Spectrum\tPeptide\tModified Peptide\tCharge\tRetention\tModification\tNumber of Sites\tObserved Mass Localization\n")
 	if e != nil {
-		msg.WriteToFile(e, "fatal")
+		msg.WriteToFile(e, "error")
 	}
 
 	// building the printing set tat may or not contain decoys
@@ -774,7 +774,7 @@ func (evi *Evidence) PSMLocalizationReport(workspace, decoyTag string, hasRazor,
 				)
 				_, e = io.WriteString(file, line)
 				if e != nil {
-					msg.WriteToFile(e, "fatal")
+					msg.WriteToFile(e, "error")
 				}
 			}
 		}
diff --git a/lib/rep/rep.go b/lib/rep/rep.go
index 46cc1345..128a49a3 100644
--- a/lib/rep/rep.go
+++ b/lib/rep/rep.go
@@ -160,7 +160,7 @@ type PSMEvidence struct {
 	MSFraggerLoc                     *id.MSFraggerLoc
 	Labels                           *iso.Labels
 	Modifications                    mod.ModificationsSlice
-	MappedProteins                   map[string]int
+	MappedProteins                   map[string]string
 	MappedGenes                      map[string]struct{}
 }
 
diff --git a/lib/rep/updater.go b/lib/rep/updater.go
index 677f3dfa..03548bd7 100644
--- a/lib/rep/updater.go
+++ b/lib/rep/updater.go
@@ -90,9 +90,17 @@ func (evi *Evidence) UpdateIonStatus(decoyTag string) {
 			// decoy by the target but it was removed because in some cases the protein
 			// does not pass the FDR filtering.
 
-			evi.PSM[i].MappedProteins[evi.PSM[i].Protein] = 0
+			evi.PSM[i].MappedProteins[evi.PSM[i].Protein] = evi.PSM[i].PrevAA + "#" + evi.PSM[i].NextAA
+
+			// recover prevAA-nextAA
+			altPrt := evi.PSM[i].MappedProteins[rp]
+			prevNext := strings.Split(altPrt, "#")
+
 			delete(evi.PSM[i].MappedProteins, rp)
+
 			evi.PSM[i].Protein = rp
+			evi.PSM[i].PrevAA = prevNext[0]
+			evi.PSM[i].PrevAA = prevNext[1]
 		}
 
 		if !evi.PSM[i].IsURazor {
@@ -106,9 +114,17 @@ func (evi *Evidence) UpdateIonStatus(decoyTag string) {
 				// decoy by the target but it was removed because in some cases the protein
 				// does not pass the FDR filtering.
 
-				evi.PSM[i].MappedProteins[evi.PSM[i].Protein] = 0
+				evi.PSM[i].MappedProteins[evi.PSM[i].Protein] = evi.PSM[i].PrevAA + "#" + evi.PSM[i].NextAA
+
+				// recover prevAA-nextAA
+				altPrt := evi.PSM[i].MappedProteins[sp]
+				prevNext := strings.Split(altPrt, "#")
+
 				delete(evi.PSM[i].MappedProteins, sp)
+
 				evi.PSM[i].Protein = sp
+				evi.PSM[i].PrevAA = prevNext[0]
+				evi.PSM[i].PrevAA = prevNext[1]
 
 				if strings.Contains(sp, decoyTag) {
 					evi.PSM[i].IsDecoy = true
@@ -749,10 +765,22 @@ func (evi *Evidence) ApplyRazorAssignment() {
 
 				evi.PSM[i].IsURazor = true
 
-				evi.PSM[i].MappedProteins[evi.PSM[i].Protein]++
+				evi.PSM[i].MappedProteins[evi.PSM[i].Protein] = evi.PSM[i].PrevAA + "#" + evi.PSM[i].NextAA
+
+				// TODO recover prev-next
+				altPrt := evi.PSM[i].MappedProteins[v.MappedProtein]
+				prevNext := strings.Split(altPrt, "#")
+
 				delete(evi.PSM[i].MappedProteins, v.MappedProtein)
+
 				evi.PSM[i].Protein = v.MappedProtein
 
+				// to avoid decoys
+				if len(prevNext) > 1 {
+					evi.PSM[i].PrevAA = prevNext[0]
+					evi.PSM[i].NextAA = prevNext[1]
+				}
+
 			}
 		}
 	}
diff --git a/lib/spc/spc.go b/lib/spc/spc.go
index 85d2b085..85e2d21d 100644
--- a/lib/spc/spc.go
+++ b/lib/spc/spc.go
@@ -58,7 +58,7 @@ func (p *PepXML) Parse(f string) {
 
 	xmlFile, e := os.Open(f)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	reader := bufio.NewReader(xmlFile)
 	decoder := xml.NewDecoder(reader)
@@ -66,7 +66,7 @@ func (p *PepXML) Parse(f string) {
 
 	var mpa MsmsPipelineAnalysis
 	if e = decoder.Decode(&mpa); e != nil {
-		msg.DecodeMsgPck(e, "fatal")
+		msg.DecodeMsgPck(e, "error")
 	}
 	err := xmlFile.Close()
 	if err != nil {
@@ -83,7 +83,7 @@ func (p *ProtXML) Parse(f string) {
 
 	xmlFile, e := os.Open(f)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	defer xmlFile.Close()
 
@@ -94,7 +94,7 @@ func (p *ProtXML) Parse(f string) {
 	decoder.CharsetReader = charset.NewReader
 
 	if e = decoder.Decode(&ps); e != nil {
-		msg.DecodeMsgPck(e, "fatal")
+		msg.DecodeMsgPck(e, "error")
 	}
 
 	p.ProteinSummary = ps
diff --git a/lib/sys/sys.go b/lib/sys/sys.go
index 1e580b29..c2421789 100644
--- a/lib/sys/sys.go
+++ b/lib/sys/sys.go
@@ -4,7 +4,6 @@ import (
 	"bufio"
 	"errors"
 	"fmt"
-	"github.com/vmihailenco/msgpack/v5"
 	"io"
 	"os"
 	"os/exec"
@@ -12,6 +11,8 @@ import (
 	"runtime"
 	"strings"
 
+	"github.com/vmihailenco/msgpack/v5"
+
 	"philosopher/lib/msg"
 )
 
@@ -28,7 +29,7 @@ func GetHome() string {
 	} else if runtime.GOOS == Linux() {
 		home = os.Getenv("HOME")
 	} else {
-		msg.Custom(errors.New("cannot define your operating system"), "fatal")
+		msg.Custom(errors.New("cannot define your operating system"), "error")
 	}
 
 	return home
@@ -43,7 +44,7 @@ func GetTemp() string {
 	} else if runtime.GOOS == Linux() {
 		tmp = "/tmp"
 	} else {
-		msg.Custom(errors.New("cannot define your operating system"), "fatal")
+		msg.Custom(errors.New("cannot define your operating system"), "error")
 	}
 
 	return tmp
@@ -53,7 +54,7 @@ func GetTemp() string {
 func VerifyTemp(f string) {
 
 	if _, err := os.Stat(f); os.IsNotExist(err) {
-		msg.Custom(errors.New("cannot find the custom temporary folder"), "fatal")
+		msg.Custom(errors.New("cannot find the custom temporary folder"), "error")
 	}
 
 }
@@ -91,27 +92,27 @@ func CopyFile(from, to string) {
 	// Open original file
 	originalFile, e := os.Open(from)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	defer originalFile.Close()
 
 	// Create new file
 	newFile, e := os.Create(to)
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 	}
 	defer newFile.Close()
 
 	// Copy the bytes to destination from source
 	_, e = io.Copy(newFile, originalFile)
 	if e != nil {
-		msg.CopyingFile(e, "fatal")
+		msg.CopyingFile(e, "error")
 	}
 
 	// Commit the file contents
 	e = newFile.Sync()
 	if e != nil {
-		msg.Custom(e, "fatal")
+		msg.Custom(e, "error")
 	}
 
 }
@@ -235,7 +236,7 @@ func FilePermission() os.FileMode {
 func Serialize(v interface{}, filename string) {
 	output, e := os.OpenFile(filename, os.O_WRONLY|os.O_CREATE|os.O_TRUNC, FilePermission())
 	if e != nil {
-		msg.WriteFile(e, "fatal")
+		msg.WriteFile(e, "error")
 		panic(e)
 	}
 	bo := bufio.NewWriter(output)
@@ -244,12 +245,12 @@ func Serialize(v interface{}, filename string) {
 	err := enc.Encode(&v)
 	errFlush := bo.Flush()
 	if errFlush != nil {
-		msg.MarshalFile(errFlush, "fatal")
+		msg.MarshalFile(errFlush, "error")
 		panic(errFlush)
 	}
 	_ = output.Close()
 	if err != nil {
-		msg.MarshalFile(err, "fatal")
+		msg.MarshalFile(err, "error")
 		panic(err)
 	}
 }
@@ -260,7 +261,7 @@ func Restore(v interface{}, filename string, silent bool) {
 		return
 	}
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 		panic(e)
 	}
 	bi := bufio.NewReader(input)
@@ -272,7 +273,7 @@ func Restore(v interface{}, filename string, silent bool) {
 		panic(errClose)
 	}
 	if err != nil && !silent {
-		msg.DecodeMsgPck(err, "fatal")
+		msg.DecodeMsgPck(err, "error")
 		panic(err)
 	}
 }
diff --git a/lib/trq/trq.go b/lib/trq/trq.go
index 7053ceeb..19072d0b 100644
--- a/lib/trq/trq.go
+++ b/lib/trq/trq.go
@@ -44,7 +44,7 @@ func New(plex string) iso.Labels {
 		o.Channel8.Mz = 121.1220
 
 	} else {
-		msg.Custom(errors.New("unknown multiplex setting, please define the plex number used in your experiment"), "error")
+		msg.Custom(errors.New("unknown multiplex setting, please define the plex number used in your experiment"), "fatal")
 	}
 
 	return o
diff --git a/lib/uti/uti.go b/lib/uti/uti.go
index 6173f9a8..8ec48274 100644
--- a/lib/uti/uti.go
+++ b/lib/uti/uti.go
@@ -87,7 +87,7 @@ func GetLabelNames(annot string) map[string]string {
 
 	file, e := os.Open(annot)
 	if e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 	defer file.Close()
 
@@ -96,19 +96,13 @@ func GetLabelNames(annot string) map[string]string {
 		// does the line has at least an iso tag?
 		if len(scanner.Text()) >= 3 {
 
-			// replace tabs and multiple spaces by single space
-			// space := regexp.MustCompile(`\s+`)
-			// line := space.ReplaceAllString(scanner.Text(), " ")
-
-			// names := strings.Split(line, " ")
-
 			names := strings.Fields(scanner.Text())
 			labels[names[0]] = names[1]
 		}
 	}
 
 	if e = scanner.Err(); e != nil {
-		msg.ReadFile(e, "fatal")
+		msg.ReadFile(e, "error")
 	}
 
 	return labels
diff --git a/lib/wrk/unix.go b/lib/wrk/unix.go
index 69024db4..e92ae6db 100644
--- a/lib/wrk/unix.go
+++ b/lib/wrk/unix.go
@@ -1,3 +1,4 @@
+//go:build !windows
 // +build !windows
 
 package wrk
@@ -16,7 +17,7 @@ func HideFile(filename string) {
 	if !strings.HasPrefix(filepath.Base(filename), ".") {
 		e := os.Rename(filename, "."+filename)
 		if e != nil {
-			msg.Custom(errors.New("cannot hide file"), "error")
+			msg.Custom(errors.New("cannot hide file"), "fatal")
 		}
 	}
 }
diff --git a/lib/wrk/win.go b/lib/wrk/win.go
index 669c23b0..d36e29fd 100644
--- a/lib/wrk/win.go
+++ b/lib/wrk/win.go
@@ -1,3 +1,4 @@
+//go:build windows
 // +build windows
 
 package wrk
@@ -13,11 +14,11 @@ import (
 func HideFile(filename string) {
 	filenameW, e := syscall.UTF16PtrFromString(filename)
 	if e != nil {
-		msg.Custom(e, "fatal")
+		msg.Custom(e, "error")
 	}
 	e = syscall.SetFileAttributes(filenameW, syscall.FILE_ATTRIBUTE_HIDDEN)
 	if e != nil {
-		msg.Custom(errors.New("Cannot hide file"), "error")
+		msg.Custom(errors.New("Cannot hide file"), "fatal")
 	}
 	return
 }
diff --git a/lib/wrk/wrk.go b/lib/wrk/wrk.go
index e0ac62d9..5e1a2d79 100644
--- a/lib/wrk/wrk.go
+++ b/lib/wrk/wrk.go
@@ -27,7 +27,7 @@ func Run(Version, Build, temp string, backup, clean, initialize, nocheck bool) {
 	}
 
 	if (initialize && backup && clean) || (initialize && backup) || (initialize && clean) || (clean && backup) {
-		msg.Custom(errors.New("this command accepts only one parameter"), "fatal")
+		msg.Custom(errors.New("this command accepts only one parameter"), "error")
 	}
 
 	if initialize {
@@ -79,7 +79,7 @@ func Init(version, build, temp string) {
 
 		os.Mkdir(da.MetaDir, sys.FilePermission())
 		if _, e := os.Stat(sys.MetaDir()); os.IsNotExist(e) {
-			msg.CreatingMetaDirectory(e, "fatal")
+			msg.CreatingMetaDirectory(e, "error")
 		}
 
 		if runtime.GOOS == sys.Windows() {
@@ -88,7 +88,7 @@ func Init(version, build, temp string) {
 
 		os.Mkdir(da.Temp, sys.FilePermission())
 		if _, e := os.Stat(da.Temp); os.IsNotExist(e) {
-			msg.LocatingTemDirecotry(e, "fatal")
+			msg.LocatingTemDirecotry(e, "error")
 		}
 
 		da.Serialize()
@@ -107,7 +107,7 @@ func Backup() {
 	}
 
 	if len(m.UUID) < 1 && len(m.Home) < 1 {
-		msg.LocatingMetaDirecotry(errors.New(""), "error")
+		msg.LocatingMetaDirecotry(errors.New(""), "fatal")
 	}
 
 	var name string
@@ -125,7 +125,7 @@ func Backup() {
 
 	e = zip.ArchiveFile(sys.MetaDir(), outFilePath, progress)
 	if e != nil {
-		msg.ArchivingMetaDirecotry(e, "error")
+		msg.ArchivingMetaDirecotry(e, "fatal")
 	}
 
 }
diff --git a/philosopher.yml b/philosopher.yml
index 9ce4b921..356543dd 100644
--- a/philosopher.yml
+++ b/philosopher.yml
@@ -57,7 +57,7 @@ Database Search:                                 # MSFragger-3.5 & Comet v201901
     calibrate_mass: 2                            # 0=Off, 1=On, 2=On and find optimal parameters
     use_all_mods_in_first_search: 0              # use all variable modifications in first search (0 for No, 1 for Yes).
     write_calibrated_mgf: 0                      # write calibrated MS2 scan to a MGF file (0 for No, 1 for Yes)
-    isotope_error: 0/1/2                         # 0=off, 0/1/2 (standard C13 error)
+    isotope_error: 0/1/2                         # 0=off, 0/1/2 (standard C13 "error")
     mass_offsets: 0                              # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue)
     restrict_deltamass_to: all                   # specify amino acids on which delta masses (mass offsets or search modifications) can occur. Allowed values are single letter codes (e.g. ACD), must
     precursor_mass_mode: selected                # one of isolated/selected/corrected.