FileNotFoundError: '.zmetadata' on variant_calls()

[jchiefelk]

This error is thrown when making a variant call from a Pv4 or Pf7 object. variant_calls(). The source of this error is in on line 80 of plamodium.py here, https://github.com/malariagen/malariagen-data-python/blob/master/malariagen_data/plasmodium.py#L80

I created an instance of Pf7 or Pv4 using a local copy of the releases, examplepf7 = malariagen_data.Pf7("/local/path/to/pf7_release/"). I did fill out the Google Form, but I didn't want to wait to get SNP data I need.

[leehart]

@eselimnl @podpearson Any ideas?

[eselimnl]

Hi @jchiefelk, it is interesting that your local copy is missing the .zmetadata files. Have you downloaded this copy from ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7.zarr.zip?

I hope you can generate the missing file yourselves with the following lines of codes:

import zarr
from zarr.storage import DirectoryStore

store = DirectoryStore("/local/path/to/pf7_release/")
zarr_group = zarr.open(store)
zarr.consolidate_metadata(store)

Please me know if you have any issues.

[jchiefelk]

@eselimnl - I downloaded the data from Figshare. I didn't have permissions to ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7.zarr.zip

[eselimnl]

Thanks for getting back. I couldn't find the genotype calls file (zarr) on figshare, to make sure please check if you have downloaded Pf7.zarr.zip. This file is publicly available for download via FTP. If you’re on a Linux/macOS system, please try:

wget -c ftp://ngs.sanger.ac.uk/production/malaria/Resource/34/Pf7.zarr.zip
Since the file is 550GB, the download may take several hours depending on your network speed.

[leehart]

Thanks @eselimnl . Hi @jchiefelk . Please let us know whether using the public FTP resource resolves your issue. Out of curiosity, did you try consolidating the metadata of your local Zarr? As @eselimnl suggests, this ought to re-generate any missing .zmetadata files.