diff --git a/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriter.java b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriter.java
index e209dfb0d..9ba3d5e7b 100644
--- a/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriter.java
+++ b/eva-accession-pipeline/src/main/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriter.java
@@ -146,7 +146,6 @@ public void open(ExecutionContext executionContext) throws ItemStreamException {
                     boolean append = false;
                     this.contigsWriter = new BufferedWriter(new FileWriter(this.contigsOutput, append));
                     this.variantsWriter = new BufferedWriter(new FileWriter(this.variantsOutput, append));
-                    executionContext.put(IS_HEADER_WRITTEN_KEY, IS_HEADER_WRITTEN_VALUE);
                 }
             }
         } catch (IOException e) {
@@ -176,7 +175,7 @@ private void loadContigMappingFromTemporaryFile(File contigMappingFile) throws I
     }
 
     public void update(ExecutionContext executionContext) throws ItemStreamException {
-
+        executionContext.put(IS_HEADER_WRITTEN_KEY, IS_HEADER_WRITTEN_VALUE);
     }
 
     public void close() throws ItemStreamException {
diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriterTest.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriterTest.java
index 3aee49e5f..493bfd446 100644
--- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriterTest.java
+++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/batch/io/AccessionReportWriterTest.java
@@ -226,6 +226,7 @@ private void writeAndResumeAndWrite(String originalChromosome1, String contig1,
         accessionReportWriter.write(Collections.singletonList(variant),
                                     GetOrCreateAccessionWrapperCreator.convertToGetOrCreateAccessionWrapper(
                                             Collections.singletonList(accessionWrapper)));
+        accessionReportWriter.update(executionContext);
         accessionReportWriter.close();
 
         // second writer