JAL-3285 fix incorrect file paths on HMMAlign/Search results

[jalview.git] / src / jalview / hmmer / HMMBuild.java

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index ee133ff..0b6e3ee 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -334,8 +334,8 @@ public class HMMBuild extends HmmerCommand
       args.add(ARG_DNA);
     }
 
-    args.add(getFilePath(hmmFile));
-    args.add(getFilePath(sequencesFile));
+    args.add(getFilePath(hmmFile, true));
+    args.add(getFilePath(sequencesFile, true));
 
     return runCommand(args);
   }