diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 095fb57b77c95ff412350e2d9594d5befc33ef96..9620e6bc6daad3f16b32745267f571348c743a22 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -263,7 +263,7 @@ object ExtractAlignedFastq extends ToolCommand {
 
       case (None, None) => extractReads(memFunc,
         new FastqReader(commandArgs.inputFastq1),
-        new BasicFastqWriter(commandArgs.inputFastq1))
+        new BasicFastqWriter(commandArgs.outputFastq1))
 
       case (Some(i2), Some(o2)) => extractReads(memFunc,
         new FastqReader(commandArgs.inputFastq1),