Repeatedly getting a EOF error when running QC on UKB imputed genotype data:
index_file_map = {file+".bgen":f'{database_dir}/tmp/'+file.split("/")[-1]+".bgen.idx2"}
hl.index_bgen([file+".bgen"], index_file_map=index_file_map)
mt = hl.import_bgen([file+".bgen"], entry_fields=["GT"], sample_file=file+".sample", index_file_map=index_file_map, n_partitions=2000)
Full error is attached and occurs at variant QC (after successful sample QC) - has anyone else encountered this error before?
Many Thanks,
Barney
Comments
1 comment
Yes, I run into something similar and provide the workaround here.
https://community.dnanexus.com/s/question/0D5t000004AflSiCAJ/hail-troubleshooting-for-ukb-data
Could you see if this solves your issue?
Please sign in to leave a comment.