First tutorial: IllegalArgumentException

Hail Query & hailctl
1

I installed using pip on Windows (including Java 8 JRE). Everything seems to work, e.g. hl.init(). The problem began with hl.utils.get_1kg('data/'), when I get Error summary: IllegalArgumentException: Wrong FS: file://C:\Users\darwell\AppData\Local\Temp\tmp2u_gs310\1kg.vcf.bgz, expected: file:///

However, the 1kg.vcf.bgz file appears in a Temp folder, so I can move it to the data folder.

But from hl.import_vcf('data/1kg.vcf.bgz').write('data/1kg.mt', overwrite=True) I get the error Error summary: IOException: (null) entry in command string: null chmod 0644 C:\Users\darwell\Desktop\work\hail\data\1kg.mt\rows\rows\parts\part-1-2-1-0-f31275e4-ec4b-ab19-4b85-b7adc12dbfd9

Although, hl.import_vcf('data/1kg.vcf.bgz') only finds the file

2

In general, Hail isn’t supported / expected to work on Windows. I don’t use a Windows computer, so not exactly sure how this works, but we do have users who go through the Linux Subsystem on Windows and manage to get it work.

3

OK thank you - I thought this might be the reason but was hopeful as it seemed to function pretty well