diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf
index bad704cbbe2..b7fa6c4d2cf 100644
--- a/modules/nf-core/mmseqs/cluster/main.nf
+++ b/modules/nf-core/mmseqs/cluster/main.nf
@@ -34,8 +34,7 @@ process MMSEQS_CLUSTER {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf
index b1d6caf0b06..ef11306895b 100644
--- a/modules/nf-core/mmseqs/createdb/main.nf
+++ b/modules/nf-core/mmseqs/createdb/main.nf
@@ -33,8 +33,7 @@ process MMSEQS_CREATEDB {
         createdb \\
         ${sequence_name} \\
         ${prefix}/${prefix} \\
-        $args \\
-        --compressed 1
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf
index 4e9c82a3499..3c8b06fa992 100644
--- a/modules/nf-core/mmseqs/createindex/main.nf
+++ b/modules/nf-core/mmseqs/createindex/main.nf
@@ -30,8 +30,7 @@ process MMSEQS_CREATEINDEX {
         \${DB_INPUT_PATH_NAME} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf
index d5afc0694ae..8fde57677f7 100644
--- a/modules/nf-core/mmseqs/createtsv/main.nf
+++ b/modules/nf-core/mmseqs/createtsv/main.nf
@@ -40,8 +40,7 @@ process MMSEQS_CREATETSV {
         \$DB_RESULT_PATH_NAME \\
         ${prefix}.tsv \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf
index 176d7b45d59..8f94eac5ffa 100644
--- a/modules/nf-core/mmseqs/databases/main.nf
+++ b/modules/nf-core/mmseqs/databases/main.nf
@@ -28,7 +28,6 @@ process MMSEQS_DATABASES {
         ${prefix}/database \\
         tmp/ \\
         --threads ${task.cpus} \\
-        --compressed 1 \\
         ${args}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/mmseqs/easysearch/main.nf b/modules/nf-core/mmseqs/easysearch/main.nf
index c934f186cbd..cd509130c7e 100644
--- a/modules/nf-core/mmseqs/easysearch/main.nf
+++ b/modules/nf-core/mmseqs/easysearch/main.nf
@@ -36,8 +36,7 @@ process MMSEQS_EASYSEARCH {
         ${prefix}.tsv \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf
index c5927985897..fb8663b98f1 100644
--- a/modules/nf-core/mmseqs/linclust/main.nf
+++ b/modules/nf-core/mmseqs/linclust/main.nf
@@ -34,8 +34,7 @@ process MMSEQS_LINCLUST {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/search/main.nf b/modules/nf-core/mmseqs/search/main.nf
index ed37960f413..3af68835b19 100644
--- a/modules/nf-core/mmseqs/search/main.nf
+++ b/modules/nf-core/mmseqs/search/main.nf
@@ -40,9 +40,7 @@ process MMSEQS_SEARCH {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
-
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mmseqs/taxonomy/main.nf b/modules/nf-core/mmseqs/taxonomy/main.nf
index 54849885691..396abd1f243 100644
--- a/modules/nf-core/mmseqs/taxonomy/main.nf
+++ b/modules/nf-core/mmseqs/taxonomy/main.nf
@@ -38,8 +38,7 @@ process MMSEQS_TAXONOMY {
         ${prefix}_taxonomy/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":