JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running

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

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 974d2b2..85abd50 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -202,7 +202,7 @@ public class HMMBuild extends HmmerCommand
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);
 
-      exportStockholm(copyArray, alignmentFile, ac);
+      exportStockholm(copyArray, alignmentFile, ac, false);
 
       recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));