AttributeError

[biostatShao]

Hi Shadi,

I hope this message finds you well. I am reaching out to address two distinct AttributeError issues I encountered while using VIPRS. Here are the details:

1. First Error:

When I run the Command Line Script (viprs_fit) with the --sumstats-format custom option, I get the following error:

--------------------  Reading input data  --------------------

Reading the training dataset...
Reading LD metadata...
Reading summary statistics...
Traceback (most recent call last):
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 657, in <module>
main()
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 601, in main
data_loaders = init_data(args)
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 163, in init_data
gdl.read_summary_statistics(args.sumstats_path,
File "/home/zhshao/anaconda3/envs/py38/lib/python3.8/site-packages/magenpy/GWADataLoader.py", line 551, in read_summary_statistics
ss_tab = SumstatsTable.from_file(f,
File "/home/zhshao/anaconda3/envs/py38/lib/python3.8/site-packages/magenpy/SumstatsTable.py", line 737, in from_file
sumstats_format_l = sumstats_format.lower()
AttributeError: 'NoneType' object has no attribute 'lower'

If I change the summary statistic format to another predefined format, such as magenpy, and then run with --sumstats-format magenpy, this AttributeError: 'NoneType' object has no attribute 'lower' does not occur. However, I encounter the following error later:

2. Second Error:

----------------------  Model fitting  -----------------------

Traceback (most recent call last):
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 657, in <module>
main()
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 609, in main
fit_results = Parallel(n_jobs=args.n_jobs)(
File "/home/zhshao/anaconda3/envs/py38/lib/python3.8/site-packages/joblib/parallel.py", line 1918, in call
return output if self.return_generator else list(output)
File "/home/zhshao/anaconda3/envs/py38/lib/python3.8/site-packages/joblib/parallel.py", line 1847, in _get_sequential_output
res = func(*args, **kwargs)
File "/home/zhshao/anaconda3/envs/py38/bin/viprs_fit", line 359, in fit_model
m = model(data_dict['train'])
File "/home/zhshao/anaconda3/envs/py38/lib/python3.8/site-packages/viprs/model/VIPRS.py", line 160, in init
self.ld_data[c], self.ld_indptr[c] = ld_mat.low_memory_load(dtype=dtype)
AttributeError: 'LDMatrix' object has no attribute 'low_memory_load'

Please note that the LD matrix is computed with the following command:

/home/zhshao/anaconda3/envs/py38/bin/magenpy_ld --estimator windowed --backend plink --ld-window-kb 1000 ......

How should I resolve these issues?

Thank you!

Zhonghe