diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index e3c9ef1..67fc46e 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "b6b18c0"
+var _Commit = "8a28c9a"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.
diff --git a/pkg/obitools/obiconvert/options.go b/pkg/obitools/obiconvert/options.go
index 5b96925..6893432 100644
--- a/pkg/obitools/obiconvert/options.go
+++ b/pkg/obitools/obiconvert/options.go
@@ -71,16 +71,15 @@ func InputOptionSet(options *getoptions.GetOpt) {
 
 }
 
-func OutputModeOptionSet(options *getoptions.GetOpt) {
+func OutputModeOptionSet(options *getoptions.GetOpt, compressed bool) {
 	options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
 		options.Description("Disable the progress bar printing"))
 
-	options.BoolVar(&__compressed__, "compress", false,
-		options.Alias("Z"),
-		options.Description("Output is compressed"))
-
-	options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
-		options.Description("Sequences of length equal to zero are suppressed from the output"))
+	if compressed {
+		options.BoolVar(&__compressed__, "compress", false,
+			options.Alias("Z"),
+			options.Description("Output is compressed"))
+	}
 
 	options.StringVar(&__output_file_name__, "out", __output_file_name__,
 		options.Alias("o"),
@@ -90,6 +89,9 @@ func OutputModeOptionSet(options *getoptions.GetOpt) {
 }
 
 func OutputOptionSet(options *getoptions.GetOpt) {
+	options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
+		options.Description("Sequences of length equal to zero are suppressed from the output"))
+
 	options.BoolVar(&__output_in_fasta__, "fasta-output", false,
 		options.Description("Write sequence in fasta format (default if no quality data available)."))
 
@@ -105,7 +107,7 @@ func OutputOptionSet(options *getoptions.GetOpt) {
 		options.Alias("O"),
 		options.Description("output FASTA/FASTQ title line annotations follow OBI format."))
 
-	OutputModeOptionSet(options)
+	OutputModeOptionSet(options, true)
 }
 
 func PairedFilesOptionSet(options *getoptions.GetOpt) {
diff --git a/pkg/obitools/obicsv/options.go b/pkg/obitools/obicsv/options.go
index cff5e4c..1928fad 100644
--- a/pkg/obitools/obicsv/options.go
+++ b/pkg/obitools/obicsv/options.go
@@ -66,7 +66,7 @@ func CSVOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	obiconvert.InputOptionSet(options)
-	obiconvert.OutputModeOptionSet(options)
+	obiconvert.OutputModeOptionSet(options, true)
 	obioptions.LoadTaxonomyOptionSet(options, false, false)
 	CSVOptionSet(options)
 }
diff --git a/pkg/obitools/obitaxonomy/options.go b/pkg/obitools/obitaxonomy/options.go
index 634e39b..85ef0ac 100644
--- a/pkg/obitools/obitaxonomy/options.go
+++ b/pkg/obitools/obitaxonomy/options.go
@@ -5,6 +5,7 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"github.com/DavidGamba/go-getoptions"
 )
 
@@ -36,6 +37,7 @@ func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 
 func OptionSet(options *getoptions.GetOpt) {
 	obioptions.LoadTaxonomyOptionSet(options, false, true)
+	obiconvert.OutputModeOptionSet(options, false)
 	FilterTaxonomyOptionSet(options)
 	options.BoolVar(&__fixed_pattern__, "fixed", false,
 		options.Alias("F"),