IndexError: tuple index out of range

[mpmorley]

Hi

As a background I converted a umich dosage file to to a plink binary using the following cmd.

plink2 --vcf chr1.dose.vcf.gz dosage=HDS --make-bed --out chr1

However markers with the same name and thus position were left in. I did recieve a warning that they were being renamed.

I ran nearly 50% of of the SNPs when this error popped up. Any hints?

Traceback (most recent call last):
  File "/anaconda3/lib/python3.6/site-packages/genetest/analysis.py", line 168, in _gwas_worker
    results = fit(y[not_missing], X[not_missing])
  File "//anaconda3/lib/python3.6/site-packages/genetest/statistics/models/survival.py", line 82, in fit
    fitted = model.fit()
  File "//anaconda3/lib/python3.6/site-packages/statsmodels/duration/hazard_regression.py", line 449, in fit
    fit_rslts = super(PHReg, self).fit(**args)
  File "//anaconda3/lib/python3.6/site-packages/statsmodels/base/model.py", line 466, in fit
    full_output=full_output)
  File "//anaconda3/lib/python3.6/site-packages/statsmodels/base/optimizer.py", line 191, in _fit
    hess=hessian)
  File "//anaconda3/lib/python3.6/site-packages/statsmodels/base/optimizer.py", line 276, in _fit_newton
    H[np.diag_indices(H.shape[0])] += ridge_factor
IndexError: tuple index out of range