Hello,
I am trying to use hail.import_plink on a bed, fam, and bim file set for my study cohort. I am working in terra workspace, using a preset (i.e., preconfigured) hail environment and spark clusters. I can confirm that my files are physically present in my workspace storage, and following a similar question in this forum, I was able to resolve the initial error:
Hail version: 0.2.130.post1-c69cd67afb8b
Error summary: RemoteException: File does not exist:
As recommended here, I modified my path to the files by adding file:/// in front of the path and it seemed to work.
However, when I run a function like hl.count or hl.filter_intervals on the resulting hail matrix table, I then get the following error:
FileNotFoundException: File file:/home/jupyter/xxx.bed does not exist.
Note that I previously created a valid hail matrix table in a standard virtual machine within terra workspace, but the hl.db_experimental function failed in that environment, which is why I moved to a configured hail environment with spark clusters. But it just doesn’t recognize the input files even though they are physically present.
Please kindly assist me with troubleshooting.
Thank you.