AssertionError: data contains observations with all missing values

[willright28]

Hi @terhorst ,

phlash.psmc return this error AssertionError: data contains observations with all missing values. The whole error mesage is:

Using 1 GPUs
Traceback (most recent call last):
File "", line 1, in
File "/root/miniconda3/envs/py312/lib/python3.12/site-packages/phlash/psmc.py", line 29, in psmc
return phlash.fit(contigs, test_data=test_data, **options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/py312/lib/python3.12/site-packages/phlash/mcmc.py", line 205, in fit
train_kern = get_kernel(
^^^^^^^^^^^
File "/root/miniconda3/envs/py312/lib/python3.12/site-packages/phlash/kernel.py", line 13, in get_kernel
return PSMCKernel(M=M, data=data, double_precision=double_precision)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/py312/lib/python3.12/site-packages/phlash/gpu.py", line 351, in init
self.gpu_kernels.append(_PSMCKernelBase(M, data, double_precision))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/py312/lib/python3.12/site-packages/phlash/gpu.py", line 111, in init
assert np.all(
AssertionError: data contains observations with all missing values

I used 8 psmcfa files as input. Does this mean that at least one chromosome in one psmcfa file contains only N value? But I've checked my psmcfa files and found that every chromosome contains T or K value.

Thanks for your time and attention!