Hello, I am trying to import by vcf file, but I am getting an error whenever I am trying to apply any function to my file. i_dir = '/Users/jeji/ASD_pQTL' vcf_path = '/'.join([i_dir, "SNUBH_ASD_210210.vcf.gz"]) mt = hl.import_vcf(vcf_path, reference_genome = 'GRCh38', force_bgz = True, min_partition…

This seems like probably a hail bug. Two things: Is this VCF private? Or is it public data? Can you try making the first line of your hail script: hl._set_flags(no_whole_stage_codegen='1') and see if that works?

It is a private VCF data! Yes, it works when I initialize hail by that code! and I have attached my log file. Thanks :smiley: hail20211217.log (312.6 KB)

Hi all, 25d I am running into a similar issue. If I use hl._set_flags(no_whole_stage_codegen=‘1’) however and initialise that way, I am then unable to intialise hail with build ‘GRCh38’. Is there a way around this? Thanks

Hey @skose ! I’m sorry to hear Hail is giving you a hard time. Can you share the full error message you get when you start hail with GRCh38 as the default genome reference?

Hi @danking Thanks for the reply. I initialise hail as per usual but then get a java error. The file is bgzipped and tabixed. When I try mt.show() it gets an error. I can do analysis on the file suck as kinship etc, but when I try to show anything it does that. The initial thread says to initialise…

You can set flags after initializing. If you set flags before initializing, that will initialize automatically (and prevent you from re-initializing with different parameters). The solution here is to move the _set_flags line after the hl.init line, I think.

Unable to utilize my vcf file

Hail Query & hailctl

johnc1231 December 16, 2021, 5:30pm 3

Can you also share the hail log file with us?

Topic		Replies	Views
FatalError: IllegalArgumentException: requirement failed (Error occured during import_vcf) Hail Query & hailctl	6	798	April 11, 2022
Import VCF from dbSNP Hail Query & hailctl	3	635	August 15, 2022
Help for finding rare variants for 100 patients Hail Query & hailctl	10	490	March 20, 2023
I cannot import the UKB 200K WGS VCFs in Hail due to an empty line in the VCF after the header lines Hail Query & hailctl	2	577	July 7, 2022
Joint genotype example vcf file Hail Query & hailctl	10	1268	May 6, 2020

Unable to utilize my vcf file

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