Zhangzzzzzy
commented
11 months ago I found the solution, just need to cull out the NA and 0 snp's in it, hope this helps anyone else who also has this problem.
Closed Zhangzzzzzy closed 11 months ago
Zhangzzzzzy
commented
11 months ago I found the solution, just need to cull out the NA and 0 snp's in it, hope this helps anyone else who also has this problem.
I carried out the process of rep1-8, however, at rep=9-10, I met the following error report:
python3 mixer/precimed/mixer.py fit1 \ --trait1-file pycharm-community-2023.2.1/packages/Mixer/MDD.csv.gz \ --out pycharm-community-2023.2.1/packages/Mixer/result/MDD.fit.rep${REP} \ --extract pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/test/test/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep${REP}.snps \ --bim-file pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ --ld-file pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ --lib mixer/src/build/lib/libbgmg.so INFO:root:init(lib_name=mixer/src/build/lib/libbgmg.so, context_id=0) INFO:root:init_log(pycharm-community-2023.2.1/packages/Mixer/result/MDD.fit.rep10.log) INFO:root:log_message(***
Call: ./mixer.py fit1 \ --out pycharm-community-2023.2.1/packages/Mixer/result/MDD.fit.rep10 \ --lib mixer/src/build/lib/libbgmg.so \ --bim-file pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ --ld-file pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ --trait1-file pycharm-community-2023.2.1/packages/Mixer/MDD.csv.gz \ --extract pycharm-community-2023.2.1/packages/ldsc/1000G_EUR_Phase3_plink/test/test/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep10.snps ) INFO:root:init(lib_name=mixer/src/build/lib/libbgmg.so, context_id=0) Traceback (most recent call last): File "/home/zhang/mixer/precimed/mixer.py", line 23, in
args.func(args)
File "/home/zhang/mixer/precimed/mixer/cli.py", line 647, in execute_fit1_or_test1_parser
results = init_results_struct(libbgmg, args)
File "/home/zhang/mixer/precimed/mixer/cli.py", line 639, in init_results_struct
results['options']['sum_weights'] = float(np.sum(libbgmg.weights))
File "/home/zhang/mixer/precimed/mixer/libbgmg.py", line 168, in weights
return self._get_vec_impl(self.cdll.bgmg_retrieve_weights, np.float32, self.num_tag, trait=None)
File "/home/zhang/mixer/precimed/mixer/libbgmg.py", line 410, in _get_vec_impl
self._check_error(func(*args))
File "/home/zhang/mixer/precimed/mixer/libbgmg.py", line 418, in _check_error
raise RuntimeError(self.get_last_error())
RuntimeError: runtime_error: arg <= 0
I don't know how to solve this problem and would appreciate an answer.