Error at value 'G': error parsing value into int32 at column id 'REF' for entry field 'x'

Hail Query & hailctl
1

Hi,

I’ve been having some trouble while performing the .write operation in the middle of of my hail compilation. I believe this step is technically a checkpoint, but I’m confused as to what I might have done in translating my data into this workflow that might cause it not to work.

The error I’m getting is:

HailUserError: Error summary: HailException: in file /path/to/file/ancnumber0.hapcount.txt on line 84501 at value ‘G’:
error parsing value into int32 at column id ‘REF’ for entry field ‘x’

Any clarification on why this error would be occurring especially during this step in processing, or potential fixes would be greatly appreciated.

Sorry for any inconvenience,
Dan

2

Hail pipelines don’t run immediately: they build up a recipe. When you write, you’re executing everything leading up to the write.

This looks like an error in one of your source files: ancnumber0.hapcount.txt. On line 84501, in the REF column, you told Hail (or Hail imputed on your behalf) that the REF column was an integer but it found the letter G.

It looks like you’re using import_matrix_table. Maybe ref should be a row field? Take a look at the first example here.

3

Thanks, for your help.

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