X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHmmerCommand.java;h=9db0ae19601e2135f00f90c221477cf0f01cf522;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=e24100811d3ea8fcfdce13e46dcd4b4114038980;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index e241008..9db0ae1 100644
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -3,6 +3,7 @@ package jalview.hmmer;
 import jalview.analysis.SeqsetUtils;
 import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -196,8 +197,8 @@ public abstract class HmmerCommand implements Runnable
       int exitValue = p.exitValue();
       if (exitValue != 0)
       {
-        Cache.log.error("Command failed, return code = " + exitValue);
-        Cache.log.error("Command/args were: " + args.toString());
+        Console.error("Command failed, return code = " + exitValue);
+        Console.error("Command/args were: " + args.toString());
       }
       return exitValue == 0; // 0 is success, by convention
     } catch (Exception e)
@@ -220,7 +221,7 @@ public abstract class HmmerCommand implements Runnable
             Cache.getProperty(Preferences.CYGWIN_PATH));
     if (bash == null)
     {
-      Cache.log.error("Cygwin shell not found");
+      Console.error("Cygwin shell not found");
       return commands;
     }