I’m trying to follow GWAS tutorial and everything works perfectly using tutorial data.
But when I run using production data, for some chromosomes, after filter_rows for QC purposes, I cannot work with my MatrixTable anymore.
mt = mt.filter_rows(mt.variant_qc.AF > 0.01)
mt = mt.filter_rows(mt.variant_qc.p_value_hwe > 1e-6)
After this process, calling MatrixTable’s count method, I’ve got this error message:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 442 in stage 2.0 failed 1 times, most recent failure: Lost task 442.0 in stage 2.0 (TID 570, localhost, executor driver): java.lang.AssertionError: assertion failed
Hail version: 0.2.16-6da0d3571629
Error summary: AssertionError: assertion failed
Can anyone help me?
Thanks in advance.