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bvilhjal / ldpred

MIT License
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IndexError: pop from empty list #136

Open chokriNao opened 4 years ago

chokriNao commented 4 years ago

Hi, I encountered this issue when I tried to use ldpred coord using 1kg EUR as reference. I tried LDpred v. 1.0.8, 1.0.11 and the develop version and all threw the same error message. the fallowing is returned by the develop version:

Coordinating datasets (Summary statistics and LD reference genotypes). 13.04%Traceback (most recent call last): File "/usr/bin/ldpred", line 11, in load_entry_point('LDpred==1.0.11', 'console_scripts', 'ldpred')() File "/usr/lib/python3.7/site-packages/ldpred/run.py", line 380, in main main_with_args(sys.argv[1:]) File "/usr/lib/python3.7/site-packages/ldpred/run.py", line 362, in main_with_args coord_genotypes.main(p_dict) File "/usr/lib/python3.7/site-packages/ldpred/coord_genotypes.py", line 625, in main debug=p_dict['debug']) File "/usr/lib/python3.7/site-packages/ldpred/coord_genotypes.py", line 443, in coordinate_datasets reference_genotype_file, snp_indices) File "/usr/lib/python3.7/site-packages/ldpred/plinkfiles.py", line 41, in parse_plink_snps next_i = ordered_snp_indices.pop() IndexError: pop from empty list

any help please!

LuHaojie818 commented 3 years ago

I have got the same question with our test data, does anyone know what's wrong?

Parsing summary statistics file: base/TOY_BASE_GWAS.assoc 100.00% SS file loaded, now sorting and storing in HDF5 file. Coordinating datasets (Summary statistics and LD reference genotypes). 4.17%Traceback (most recent call last): File "/mnt/luhaojie/.local/bin/ldpred", line 8, in sys.exit(main()) File "/mnt/luhaojie/.local/lib/python3.8/site-packages/ldpred/run.py", line 380, in main main_with_args(sys.argv[1:]) File "/mnt/luhaojie/.local/lib/python3.8/site-packages/ldpred/run.py", line 362, in main_with_args coord_genotypes.main(p_dict) File "/mnt/luhaojie/.local/lib/python3.8/site-packages/ldpred/coord_genotypes.py", line 620, in main coordinate_datasets(p_dict['gf'], h5f,summary_dict, File "/mnt/luhaojie/.local/lib/python3.8/site-packages/ldpred/coord_genotypes.py", line 442, in coordinate_datasets raw_snps, freqs = plinkfiles.parse_plink_snps( File "/mnt/luhaojie/.local/lib/python3.8/site-packages/ldpred/plinkfiles.py", line 41, in parse_plink_snps next_i = ordered_snp_indices.pop() IndexError: pop from empty list

OmegaPetrazzini commented 3 years ago

Same error, did you find any solution?

erez-odna commented 3 years ago

getting same error, i'll be happy to know if anyone found a solution