Why Athena cannot output all the data even the data scanned is the right size?

There are several potential reasons why Athena might not be outputting all the data even when the data scanned appears to be the correct size:

1. Partition issues: If your table has many partitions, Athena might be experiencing difficulties processing all of them. This can happen especially when the partition columns are not of type 'string'. Athena prunes partitions more efficiently at the metastore level for 'string' type partitions. Consider changing your partition columns to 'string' type if they aren't already.

2. File format: While JSON is a supported format, it's not as efficient as columnar formats like Parquet or ORC. These columnar formats allow Athena to read only the required columns and often include metadata that can optimize query performance. Converting your data to Parquet or ORC might improve both the accuracy and performance of your queries.

3. Data consistency: Ensure that all your JSON files are properly formatted and consistent. Malformed JSON or inconsistencies in the data structure could cause Athena to skip certain records.

4. Query timeout: If your table has a very large number of partitions or a complex structure, the query might be timing out before it can process all the data. You might need to optimize your query or consider breaking it into smaller, more manageable chunks.

5. Hidden files: Athena treats files starting with underscores or dots as hidden. Make sure your data files don't start with these characters, as they might be ignored during the query execution.

6. File size limitations: Athena has limitations on the size of a single row or its columns (32 MB) and the size of a single line in a text file (200 MB). If your JSON data exceeds these limits, it could cause issues with data retrieval.

To improve the situation, consider the following steps:

1. Convert your data to a columnar format like Parquet or ORC.
2. Ensure your partition columns are of type 'string'.
3. Verify the consistency and format of your JSON files.
4. Check for any hidden files in your S3 bucket.
5. Review your partitioning strategy to ensure it's optimized for your query patterns.

If the problem persists after trying these steps, you may need to reach out to AWS support for further assistance, as there could be specific issues related to your data or Athena configuration.
Sources
Considerations and limitations for SQL queries in Amazon Athena - Amazon Athena
Community | What happens when you run a query in Amazon Athena?