Error summary: HailException

Hail Query & hailctl
#1

Hey,
I’m trying to run a logistic regression on my matrix table:

gwas = hl.logistic_regression_rows(test='wald',
                                  y=hl.int(mt_filtered.pheno["Sel Related Thrombocytopenia"]),
                                  x=mt_filtered.GT.n_alt_alleles(),
                                  covariates=cov)

p = hl.plot.manhattan(gwas.p_value)
show(p)

but, I keep getting this error:

Hail version: 0.2.82-2ab242915c2c
Error summary: HailException: expected 294 fields, but found 295 fields

I passed quote=’"’ to the import_table, but still with no change.

please help me :slight_smile:
thanks!
Shiri

#2

This is a problem with table import, so the logistic regression isn’t an important part of debugging the pipeline. What’s the code you use to import your table?

Also, upgrading to the latest version would be good, because the error message might be slightly different.

#3

Hi,
the import table code is:

table = hl.import_table("meta_data/023-BOSTON_samples_edited.csv", impute=True, key="USUBJID", delimiter=',', quote='"')

I filled all the null etries with 0. Now I’m getting this error:
Error summary: HailException: No complete samples: each sample is missing its phenotype or some covariate

What could be the problem?..