Hi,
I have a plink binary file (.bed,.bim,.fam) that is on GRCh38 and I am trying to use hail to liftover it to GRCh37. The .bed file is about 25GB. There are 71267 samples and 1414695 variants.
I used mt = hl.methods.import_plink() to read in the plink file. After the liftover is done, I was using hl.export_plink() to export the lifted mt back to plink binary file. It has been 4 hours but the exporting step is still running without generating any output. There is no error message. But there is one INFO:
2025-04-23 16:42:22 Hail: INFO: Ordering unsorted dataset with network shuffle.
I really appreciate your input here. Thank you very much!