ValueError: column index exceeds matrix dimensions

[hsymoon]

Hi eveyone,
I want to verify the best donor numbers of my vcf-data,which is the outputs of cellsnp-lite. I tried the demo command developers provided as follows:
`cell_vcf = vireoSNP.load_VCF('batch1_cellSNP.cells.vcf.gz', biallelic_only=True)

cell_dat = vireoSNP.vcf.read_sparse_GeneINFO(cell_vcf['GenoINFO'], keys=['AD', 'DP'])

AD = cell_dat['AD']

DP = cell_dat['DP']

n_donor_list = np.arange(2, 7)

ELBO_list_all = []

for _n_don in n_donor_list:
res = vireoSNP.vireo_wrap(AD, DP, n_donor=_n_don, learn_GT=True,
n_extra_donor=0, ASE_mode=False, fix_beta_sum=False,
n_init=50, check_doublet=True, random_seed=1)
ELBO_list_all.append(res['LB_list']) `

but I got the reply as follows:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/public/home/syhou/miniconda3/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/vireoSNP/utils/vireo_wrap.py", line 17, in _model_fit
_model.fit(AD, DP, min_iter=5, max_iter=max_iter,
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/vireoSNP/utils/vireo_model.py", line 313, in fit
ELBO += np.sum(get_binom_coeff(AD, DP))
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/vireoSNP/utils/vireo_base.py", line 15, in get_binom_coeff
_AD = AD[idx].astype(np.int64)
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_index.py", line 44, in getitem
row, col = self._validate_indices(key)
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_index.py", line 147, in _validate_indices
row, col = _unpack_index(key)
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_index.py", line 272, in _unpack_index
return index.nonzero()
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_base.py", line 826, in nonzero
A = self.tocoo()
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_compressed.py", line 1040, in tocoo
return self._coo_container(
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_coo.py", line 204, in init
self._check()
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/scipy/sparse/_coo.py", line 293, in _check
raise ValueError('column index exceeds matrix dimensions')
ValueError: column index exceeds matrix dimensions
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "", line 2, in
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/vireoSNP/utils/vireo_wrap.py", line 83, in vireo_wrap
_models_all = [res.get() for res in result]
File "/public/home/syhou/miniconda3/lib/python3.10/site-packages/vireoSNP/utils/vireo_wrap.py", line 83, in
_models_all = [res.get() for res in result]
File "/public/home/syhou/miniconda3/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: column index exceeds matrix dimensions

It is so sad,here is my information of vcf_data used :
Number of samples: 9809
Number of SNPs: 14131
Number of INDELs: 0
Number of MNPs: 0
Number of others: 0
Number of sites: 14131

Can you help me , Thanks for replying

[huangyh09]

Thanks for sharing the issue. While you shared the info in the VCF file, can you still try print(cell_dat['AD'].shape)?

[hsymoon]

print(cell_dat['AD'].shape)

Hello,here is the command output:
print(cell_dat['AD'].shape) (14131, 9809)
Thanks for helping me

[huangyh09]

Thanks. This looks normal. Can you further try?

from vireoSNP.utils.vireo_base import get_binom_coeff, logbincoeff

np.sum(get_binom_coeff(AD, DP))

np.sum(logbincoeff(DP, AD, is_sparse=True))