diff --git a/build/popins2.o b/build/popins2.o
index be9b8f36e21ae877e3a5db754769f04a9383bc5b..1363e9adcd4aaeb6dc12583d9c38d95d8dfd702c 100644
Binary files a/build/popins2.o and b/build/popins2.o differ
diff --git a/popins2 b/popins2
index 9845c2fb429527ac9b60c014eaecd5a92d4fd03c..1f24a555bc2acc0427f0dd1cd133ed2b9242d721 100755
Binary files a/popins2 and b/popins2 differ
diff --git a/src/argument_parsing.h b/src/argument_parsing.h
index a893a23be07be0e36bcb3dead3dc521bde5a7c25..cb4522a51a7c2bbc7113d22776fc1075762076ee 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -1336,16 +1336,24 @@ ArgumentParser::ParseResult checkInput(MergeSetMateOptions & options){
         std::cerr << "ERROR: Path to sample directories \'" << options.prefix << "\' does not exist." << std::endl;
         res = ArgumentParser::PARSE_ERROR;
     }
-
-    if (!exists(options.nonRefBam))
+    CharString filename = options.prefix;
+    filename += "/";
+    filename += options.sampleID;
+    filename += "/";
+    filename += options.nonRefBam;
+    if (!exists(filename))
     {
-        std::cerr << "ERROR: Input BAM file \'" << options.nonRefBam << "\' does not exist." << std::endl;
+        std::cerr << "ERROR: Input BAM file \'" << filename << "\' does not exist." << std::endl;
         res = ArgumentParser::PARSE_ERROR;
     }
-
-    if (!exists(options.remappedBam))
+    filename = options.prefix;
+    filename += "/";
+    filename += options.sampleID;
+    filename += "/";
+    filename += options.remappedBam;
+    if (!exists(filename))
     {
-        std::cerr << "ERROR: Input BAM file \'" << options.remappedBam << "\' does not exist." << std::endl;
+        std::cerr << "ERROR: Input BAM file \'" << filename << "\' does not exist." << std::endl;
         res = ArgumentParser::PARSE_ERROR;
     }