diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index 863b344ee..1146c76ea 100755 --- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -536,8 +536,11 @@ class UnmatchedArgumentException extends ArgumentException { private static String formatArguments( ArgumentMatch invalidValues ) { StringBuilder sb = new StringBuilder(); for( int index: invalidValues.indices.keySet() ) - for( String value: invalidValues.indices.get(index) ) + for( String value: invalidValues.indices.get(index) ) { sb.append( String.format("%nInvalid argument value '%s' at position %d.", value, index) ); + if(value != null && Utils.dupString(' ',value.length()).equals(value)) + sb.append(" Please make sure any line continuation backslashes on your command line are not followed by whitespace."); + } return sb.toString(); } }