From a2f62ee20ac7c214730e74525d85557771c81249 Mon Sep 17 00:00:00 2001
From: Milot Mirdita <milot@mirdita.de>
Date: Tue, 2 Apr 2024 22:30:54 +0900
Subject: [PATCH] pass correct parameter list to mergeresultsbyset

---
 data/structuresearch.sh          | 2 +-
 src/workflow/StructureSearch.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/structuresearch.sh b/data/structuresearch.sh
index 4e366c7c..ab00e550 100644
--- a/data/structuresearch.sh
+++ b/data/structuresearch.sh
@@ -65,7 +65,7 @@ if [ "$ALIGNMENT_ALGO" = "tmalign" ]; then
     if [ -n "${EXPAND}" ]; then
         if notExists "${TMP_PATH}/strualn_expanded.dbtype"; then
             # shellcheck disable=SC2086
-            "$MMSEQS" mergeresultsbyset  "${INTERMEDIATE}" "${TARGET_ALIGNMENT}_clu" "${TMP_PATH}/strualn_expanded" ${MERGERESULTBYSET_PAR} \
+            "$MMSEQS" mergeresultsbyset "${INTERMEDIATE}" "${TARGET_ALIGNMENT}_clu" "${TMP_PATH}/strualn_expanded" ${MERGERESULTBYSET_PAR} \
                 || fail "Expand died"
         fi
         INTERMEDIATE="${TMP_PATH}/strualn_expanded"
diff --git a/src/workflow/StructureSearch.cpp b/src/workflow/StructureSearch.cpp
index 29f219b5..fb180b5e 100644
--- a/src/workflow/StructureSearch.cpp
+++ b/src/workflow/StructureSearch.cpp
@@ -216,7 +216,7 @@ int structuresearch(int argc, const char **argv, const Command &command) {
                     EXIT(EXIT_FAILURE);
                 }
             }
-            cmd.addVariable("MERGERESULTBYSET_PAR", par.createParameterString(par.threadsandcompression).c_str());
+            cmd.addVariable("MERGERESULTBYSET_PAR", par.createParameterString(par.mergeresultsbyset).c_str());
             cmd.addVariable("EXPAND", "1");
         }
         std::string program = tmpDir + "/structuresearch.sh";