bug fix

src/main/java/org/embl/gbcs/je/jemultiplexer/JemultiplexerIllumina.java

@@ -646,7 +646,7 @@ public class JemultiplexerIllumina extends AbstractJemultiplexer {
 			if(INDEX_FILE2.getAbsolutePath().equals(FASTQ_FILE1.getAbsolutePath()))
 				messages.add("FASTQ_FILE1 and INDEX_FILE2 are the same file !");
 			
-			if(INDEX_FILE2.getAbsolutePath().equals(FASTQ_FILE2.getAbsolutePath()))
+			if(RUNNING_PAIRED_END && INDEX_FILE2.getAbsolutePath().equals(FASTQ_FILE2.getAbsolutePath()))
 				messages.add("FASTQ_FILE2 and INDEX_FILE2 are the same file !");
 			
 			

src/main/resources/log4j.xml

-<?xml version="1.0" encoding="UTF-8" ?>
-<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
-
-<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">
-
-	<appender name="CONSOLE" class="org.apache.log4j.ConsoleAppender">
-		<layout class="org.apache.log4j.PatternLayout">
-			<param name="ConversionPattern" value="%d{dd-MM-yy HH:mm:ss} %-5p [%t] %c{1}.%M(%L) | %m%n" />
-		</layout>
-	</appender>
-
-	
-	
-	<root>
-		<level value="${log.level}" /> 
-		<appender-ref ref="CONSOLE" />
-	</root>
-
-</log4j:configuration>