For --sumstats parameter I am inputting the polyfun.py output but I believe the way I have written my input path and file name for --out-prefix might be incorrect. I am just writing the main body of the filename before the chromosome. This is the error I am getting:
[INFO] Aggregating results...
0it [00:00, ?it/s]
Traceback (most recent call last):
File "/rds/general/user/aa19618/home/polyfun/aggregate_finemapper_results.py", line 113, in
main(args)
File "/rds/general/user/aa19618/home/polyfun/aggregate_finemapper_results.py", line 53, in main
raise IOError(err_msg + '.\nTo override this error, please provide the flag --allow-missing-jobs')
OSError: output file for chromosome 1 bp 1-3000001 doesn't exist.
To override this error, please provide the flag --allow-missing-jobs
However, that file exists within the folder specified - SVD_Sargurupremraj2022_ADvas_AAA_20240422_hg19.1.chr1.1_3000001.gz
Hi there,
I am currently trying to aggregate the results using aggregate_finemapper_results.py function. This is what I run:
python ~/polyfun/aggregate_finemapper_results.py \ --out-prefix susie_output/SVD_Sargurupremraj2022_ADvas_AAA_20240422_hg19.1. \ --sumstats polyfun_output/SVD_Sargurupremraj2022_ADvas_AAA_20240422_hg19.1.snpvar_ridge_constrained.gz \ --out aggregate_results/SVD_Sargurupremraj2022_ADvas_AAA_20240422_hg19.1.agg.txt.gz
For --sumstats parameter I am inputting the polyfun.py output but I believe the way I have written my input path and file name for --out-prefix might be incorrect. I am just writing the main body of the filename before the chromosome. This is the error I am getting:
[INFO] Aggregating results... 0it [00:00, ?it/s] Traceback (most recent call last): File "/rds/general/user/aa19618/home/polyfun/aggregate_finemapper_results.py", line 113, in
main(args)
File "/rds/general/user/aa19618/home/polyfun/aggregate_finemapper_results.py", line 53, in main
raise IOError(err_msg + '.\nTo override this error, please provide the flag --allow-missing-jobs')
OSError: output file for chromosome 1 bp 1-3000001 doesn't exist.
To override this error, please provide the flag --allow-missing-jobs
However, that file exists within the folder specified - SVD_Sargurupremraj2022_ADvas_AAA_20240422_hg19.1.chr1.1_3000001.gz
Thank you in advance! Aydan