Error: "No content to map due to end-of-input"

Hello,

In this run with over 5K gvcfs,

hl.experimental.run_combiner(inputs, out_file=output_file, tmp_path=temp_bucket, branch_factor=100, batch_size=100, reference_genome=‘GRCh38’, use_genome_default_intervals=True)

I got an error message :

JsonMappingException: No content to map due to end-of-input

This error occurred in the second round which is to merge 51 MTs to 1 MTs.

Please let me know how to solve this. Thank you.
-Jina

Hello,

If you need more information for solving this issue, please let me know. Thank you.

-Jina

Jina,

This indicates that something has gone wrong with the metadata files in the matrix tables, unfortunately our current information does not say which file caused the issue.

This error seems to indicate that the metadata file is truncated or empty. I have no idea how this happened.

You may be able to figure out which file was the issue by going through all the intermediate matrix tables that have been written, finding the metadata.json.gz file in the root of each of the matrix table directories and decompressing them to see which one is empty or invalid.

Best,
Chris

Hi @chrisvittal,

Thank you so much for your advice. It could be a good starting point for solving this issue.

-Jina

Hi @chrisvittal

Fortunately, the run_combiner job with over 5k gvcfs was done successfully after I just increased the boot-dist-size from 200G to 1T as below.

–worker-boot-disk-size=1000 --preemptible-worker-boot-disk-size=1000

By the way, when I checked metadata.json.gz followed by your advice, I noticed that some tasks have 0 counts in my job as below. I wonder how to interpret it. Should I worry about 0?

Thank you.

-Jina