diff --git a/data/guidedNuclAssemble.sh b/data/guidedNuclAssemble.sh
index 4b00f73c..d7e2448b 100644
--- a/data/guidedNuclAssemble.sh
+++ b/data/guidedNuclAssemble.sh
@@ -103,7 +103,7 @@ while [ $STEP -lt $NUM_IT ]; do
 
     # 3. Ungapped alignment protein 2 nucl
     if notExists "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP.done"; then
-        "$MMSEQS" proteinaln2nucl "$INPUT_NUCL" "$INPUT_NUCL" "$INPUT_AA"  "$INPUT_AA"  "${TMP_PATH_GUIDED_ASSEMBLY}/aln_$STEP" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP"  \
+        "$MMSEQS" proteinaln2nucl "$INPUT_NUCL" "$INPUT_NUCL" "$INPUT_AA"  "$INPUT_AA"  "${TMP_PATH_GUIDED_ASSEMBLY}/aln_$STEP" "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_$STEP"  "${PROTEIN_ALN_2_NUCL_PAR}" \
             || fail "Ungapped alignment 2 nucl step died"
         deleteIncremental "$PREV_ALN_NUCL"
         touch "${TMP_PATH_GUIDED_ASSEMBLY}/aln_nucl_${STEP}.done"
diff --git a/src/workflow/GuidedNuclassembler.cpp b/src/workflow/GuidedNuclassembler.cpp
index 58061341..25689045 100644
--- a/src/workflow/GuidedNuclassembler.cpp
+++ b/src/workflow/GuidedNuclassembler.cpp
@@ -157,6 +157,8 @@ int guidedNuclAssemble(int argc, const char **argv, const Command &command) {
     bool addBacktrace = par.addBacktrace;
     par.addBacktrace = true;
     cmd.addVariable("UNGAPPED_ALN_PAR", par.createParameterString(par.rescorediagonal).c_str());
+    cmd.addVariable("PROTEIN_ALN_2_NUCL_PAR", par.createParameterString(par.proteinaln2nucl).c_str());
+
 
     // # 3. Assembly: Extend by left and right extension
     par.seqIdThr = par.multiSeqIdThr.nucleotides;