Problem with par region - infinite task

Hail Query & hailctl
1

Hi,

I have some issues using .locus.in_x_par()

the job never end, I always got 1 or few tasks that run without ending… any idea what could be the problem ?

HAIL version 0.2.32-a5876a0a2853

# Load genotype
mt_gt = hl.read_matrix_table('s3://mydata.mt')
# chrX
mt_chrX = hl.filter_intervals(mt_gt, [hl.parse_locus_interval('chrX', reference_genome='GRCh38')])
# chrX par
mt_chrX_par = mt_chrX.filter_rows(mt_chrX.locus.in_x_par())
mt_chrX_par.count_rows()

P.S. I encounter the same problem of infinite task using ld_prune()…

2

Please update to the latest version of hail. You’re more than 20 versions behind at this point, it’s possible your problem would be resolved by updating.