diff --git a/src/search.cpp b/src/search.cpp
index 171724b66..38742cf74 100644
--- a/src/search.cpp
+++ b/src/search.cpp
@@ -208,7 +208,7 @@ void argConv0(LambdaOptions & options)
 
     // query file
     if (options.qryOrigAlphabet ==
-        AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --query-alphabet
+        AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --input-alphabet
     {
         myPrint(options, 1, "Detecting query alphabet... ");
         options.qryOrigAlphabet = detectSeqFileAlphabet(options.queryFile);
diff --git a/src/shared_misc.hpp b/src/shared_misc.hpp
index 7211a6908..573d65e1a 100644
--- a/src/shared_misc.hpp
+++ b/src/shared_misc.hpp
@@ -94,8 +94,8 @@ inline AlphabetEnum detectSeqFileAlphabet(std::string const & path)
     else if (all_valid<bio::alphabet::dna15>(seq))
     {
         std::cerr << "\nWARNING: You query file was detected as non-standard DNA, but it could be AminoAcid, too.\n"
-                     "To explicitly read as AminoAcid, add '--query-alphabet aminoacid'.\n"
-                     "To ignore and disable this warning, add '--query-alphabet dna5'.\n";
+                     "To explicitly read as AminoAcid, add '--input-alphabet aminoacid'.\n"
+                     "To ignore and disable this warning, add '--input-alphabet dna5'.\n";
         return AlphabetEnum::DNA5;
     }
     else if (all_valid<bio::alphabet::aa27>(seq))