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getian107 / PRScsx

Cross-population polygenic prediction
MIT License
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error "not reading the --n_gwas parameter" #36

Closed sevi2018 closed 9 months ago

sevi2018 commented 10 months ago

Hello, I am trying to run PRScsx but keep getting the same error, I have tried everything space, and different order of parameters in the command but keep getting the same error.

./PRScsx.py --ref_dir=./reference/ --bim_prefix=./test_data/all_chrs.Q6.bim --sst_file=./test_data/EUR_OD_exposed_cases_controls.txt, ./test_data/AFR_OD_exposed_cases_controls.txt --n_gwas=5500,2300 --pop=EUR,AFR --out_dir=./output_files/ --out_name=chr22 --chrom=22 --phi=1E-02

Do you see anything wrong in this command?

Thank you in advance

getian107 commented 10 months ago

Hi - Could you try removing the space after the comma when specifying the summary stats using --sst_file and see if this resolves the issue?

sevi2018 commented 10 months ago

Thank you for your response, it works now

On Wed, Nov 15, 2023 at 8:20 PM Tian Ge @.***> wrote:

Hi - Could you try removing the space after the comma when specifying the summary stats using --sst_file and see if this resolves the issue?

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