Missing chunk of data written to file - Spring Batch FlatFileItemWriter

Question

In my application I have used RepositoryItemReader and FlatFileItemWriter The components are as follows

@Component
@StepScope
public class MyItemReader extends RepositoryItemReader<MyEntity> {

    public MyItemReader(MyEntityRepository repository) throws Exception {
        super();      

        this.setRepository(repository);
        this.setPageSize(1000);
        Map<String, Sort.Direction> sort = new HashMap<>();
        sort.put("id", Sort.Direction.ASC);
        this.setSort(sort);      
        this.setMethodName("findAll");
        this.afterPropertiesSet();
    }

}

@Component
@StepScope
public class MyItemProcessor implements ItemProcessor<MyEntity, String> {

    private final MyEntityRepository repository;

    public MyItemProcessor(MyEntityRepository repository) {
        this.repository = repository;
    }

    @Override
    public String process(MyEntity item) {
        // our business logic to convert item into string(line)
        // updating the file generated status in the fb before returning
    }
}

@Component
@StepScope
public class MyItemWriter extends FlatFileItemWriter<String> {
    public MyItemWriter(@Value("#{jobParameters['fileName']}") String fileName) throws Exception {
        this.setResource(new FileSystemResource(String.format("batch_files/%s", fileName)));
       this.setLineAggregator(new PassThroughLineAggregator<>());
       this.afterPropertiesSet();
    }
}

 @Bean
 public Step step(JobRepository jobRepository,
                                   PlatformTransactionManager transactionManager,
                                   MyItemReader myItemReader,
                                   MyItemProcessor myItemProcessor,
                                   MyItemWriter myItemWriter) {
        return new StepBuilder("fileGenerationStep", jobRepository)
                .<MyEntity, String>chunk(5000, transactionManager)               
                .reader(myItemReader)
                .processor(myItemProcessor)
                .writer(myItemWriter)
                .build();
}

@Bean
Job job(JobRepository jobRepository,
                       Step step) {
        return new JobBuilder("fileJob", jobRepository)
                .incrementer(new RunIdIncrementer())
                .start(step)               
                .build();
}

The problem is I have 12703 records in database. But I can see only 7703 records written to output file. Exactly chunk size(5000) data is missing in the output file.

I have tried adding chunk listener

@Log4j2
public class MyChunkListener implements ChunkListener {
    private int counter;

    @Override
    public void afterChunk(ChunkContext context) {
        log.info("Completed chunks: {}, Chunk complete status: {}", counter, context.isComplete());
    }

    @Override
    public void beforeChunk(ChunkContext context) {
        log.info("Chunk started, Context:  {}", context.getStepContext().getStepExecutionContext());
        counter++;
    }

    @Override
    public void afterChunkError(ChunkContext context) {
        log.info("Chunk failed, Context:  {}", context.getStepContext().getStepExecutionContext());
        log.error("Chunk number " + counter + " failed");
    }

}

 @Bean
 public Step step(JobRepository jobRepository,
                                   PlatformTransactionManager transactionManager,
                                   MyItemReader myItemReader,
                                   MyItemProcessor myItemProcessor,
                                   MyItemWriter myItemWriter) {
        return new StepBuilder("fileGenerationStep", jobRepository)
                .<MyEntity, String>chunk(5000, transactionManager)
                .listener(new MyChunkListener())
                .reader(myItemReader)
                .processor(myItemProcessor)
                .writer(myItemWriter)
                .build();
}

I have expected to see chunk number [counter] failed.

But I didn't see any logs related chunk failure.

I found only 2 chunks of data written, I am unable to find what happens the other chunk of data. It should be 3 chunks of data

I have even tried chaning the scope of itemreader and itemwriter from stepscope to jobscope, but nothing worked.