diff --git a/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp b/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp
index e654ff6e..65215f4e 100644
--- a/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp
+++ b/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp
@@ -228,8 +228,8 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB,
         IndexTable indexTable(adjustAlphabetSize, kmerSize, false);
         SequenceLookup *sequenceLookup = NULL;
         IndexBuilder::fillDatabase(&indexTable,
-                                   (maskMode == 1 || maskLowerCase == 1) ? &sequenceLookup : NULL,
-                                   (maskMode == 0 && maskLowerCase == 0) ? &sequenceLookup : NULL,
+                                   (maskMode == 1 || maskNrepeats > 0  || maskLowerCase == 1) ? &sequenceLookup : NULL,
+                                   (maskMode == 0 && maskNrepeats == 0 && maskLowerCase == 0) ? &sequenceLookup : NULL,
                                    *subMat, s3, s2, &seq, dbr1, dbFrom, dbFrom + dbSize, kmerThr,
                                    maskMode, maskLowerCase, maskProb, maskNrepeats, targetSearchMode);
         indexTable.printStatistics(subMat->num2aa);
diff --git a/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp b/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp
index d84b63a7..f07fed84 100644
--- a/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp
+++ b/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp
@@ -404,7 +404,8 @@ int prefilterInternal(int argc, const char **argv, const Command &command, int m
     if (par.gpu == true) {
         const bool isGpuDb = DBReader<unsigned int>::getExtendedDbtype(tdbr->getDbtype()) & Parameters::DBTYPE_EXTENDED_GPU;
         if (isGpuDb == false) {
-            Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db2) << " is not a valid GPU database\n";
+            Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db2) << " is not a valid GPU database\n" 
+                                << "Please call: makepaddedseqdb " << FileUtil::baseName(par.db2) << " " << FileUtil::baseName(par.db2) << "_pad\n";
             EXIT(EXIT_FAILURE);
         }
     }
diff --git a/lib/mmseqs/src/util/gpuserver.cpp b/lib/mmseqs/src/util/gpuserver.cpp
index 657edeba..db4887f2 100644
--- a/lib/mmseqs/src/util/gpuserver.cpp
+++ b/lib/mmseqs/src/util/gpuserver.cpp
@@ -31,7 +31,8 @@ int gpuserver(int argc, const char **argv, const Command& command) {
 
     const bool isGpuDb = DBReader<unsigned int>::getExtendedDbtype(dbr->getDbtype()) & Parameters::DBTYPE_EXTENDED_GPU;
     if (isGpuDb == false) {
-        Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db1) << " is not a valid GPU database\n";
+        Debug(Debug::ERROR) << "Database " << FileUtil::baseName(par.db1) << " is not a valid GPU database\n"
+                            << "Please call: makepaddedseqdb " << FileUtil::baseName(par.db2) << " " << FileUtil::baseName(par.db2) << "_pad\n";
         EXIT(EXIT_FAILURE);
     }