Traceback (most recent call last):
File "/data/conda_envs/gsMap/bin/gsmap", line 7, in
sys.exit(main())
^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/main.py", line 13, in main
args.func(args)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 131, in wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 211, in wrapper
func(*args, **kwargs)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 1479, in gwas_format_from_cli
gwas_format(config)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/format_sumstats.py", line 422, in gwas_format
gwas = gwas_checkformat(gwas, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/format_sumstats.py", line 189, in gwas_checkformat
gwas["Z"] = np.sqrt(chi2.isf(gwas.P, 1)) * np.where(gwas["BETA"] < 0, -1, 1)
^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/scipy/stats/_distn_infrastructure.py", line 2362, in isf
cond1 = (0 < q) & (q < 1)
^^^^^
TypeError: '>' not supported between instances of 'str' and 'int'
I have checked the original sumary statistics file, and made sure that there is no NA in the p_value column. Please help me to solve the problem.
Thanks a lot~
Traceback (most recent call last):
File "/data/conda_envs/gsMap/bin/gsmap", line 7, in
sys.exit(main())
^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/main.py", line 13, in main
args.func(args)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 131, in wrapper
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 211, in wrapper
func(*args, **kwargs)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/config.py", line 1479, in gwas_format_from_cli
gwas_format(config)
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/format_sumstats.py", line 422, in gwas_format
gwas = gwas_checkformat(gwas, config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/gsMap/format_sumstats.py", line 189, in gwas_checkformat
gwas["Z"] = np.sqrt(chi2.isf(gwas.P, 1)) * np.where(gwas["BETA"] < 0, -1, 1)
^^^^^^^^^^^^^^^^^^^
File "/data/conda_envs/gsMap/lib/python3.12/site-packages/scipy/stats/_distn_infrastructure.py", line 2362, in isf
cond1 = (0 < q) & (q < 1)
^^^^^
TypeError: '>' not supported between instances of 'str' and 'int'
I have checked the original sumary statistics file, and made sure that there is no NA in the p_value column. Please help me to solve the problem.
Thanks a lot~