ERROR: fine_map() missing 1 required positional argument: 'prior_chisq'
Closed this issue · 3 comments
Dear developer:
Thanks a lot for developing such a tool for TWAS and fine mapping. However, I encountered some errors when running the code, which may need your help. The error type is: fine_map() missing 1 required positional argument: 'prior_chisq'.
Here is my code:
python .\ma-focus-master\bin\focus finemap EA_WBC_new_munged_chr1.tsv:AA_WBC_new_munged_chr1.tsv 1000G.AFR.QC.allelesAligned.1:1000G.AFR.QC.allelesAligned.1 ea_fusion_genoa.db:aa_fusion_genoa.db --chr 1 --locations 37:EUR-AFR --out wbc_mafocus_chr1
And here is the log:
Starting log...
[2023-06-25 10:11:26 - INFO] Detecting 2 populations for fine-mapping.
[2023-06-25 10:11:26 - INFO] As a result, running single-population FOCUS on each population, and then Multi-ancestry FOCUS across all populations.
[2023-06-25 10:11:26 - INFO] Preparing GWAS summary file for population at EA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:27 - INFO] Preparing GWAS summary file for population at AA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:30 - INFO] Preparing reference SNP data for population at 1000G.AFR.QC.allelesAligned.1.
[2023-06-25 10:11:31 - INFO] Preparing reference SNP data for population at 1000G.AFR.QC.allelesAligned.1.
[2023-06-25 10:11:34 - INFO] Preparing weight database at ea_fusion_genoa.db.
[2023-06-25 10:11:34 - INFO] Preparing weight database at aa_fusion_genoa.db.
[2023-06-25 10:11:34 - INFO] Preparing user-defined locations at 37:EUR-AFR.
[2023-06-25 10:11:34 - INFO] Found 1278 independent regions on the entire genome.
[2023-06-25 10:11:34 - INFO] 99 independent regions currently used after being filtered on chromosome, start, and stop.
[2023-06-25 10:11:34 - INFO] Preparing data at region 1:10583-1:2880092. Skipping if following warning occurs.
[2023-06-25 10:11:34 - INFO] Deciding prior probability for a gene to be causal.
[2023-06-25 10:11:35 - INFO] Using gencode file prior probability 0.005988023952095809.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:10583-1:2880092 at EA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:10583-1:2880092 at AA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:10583-1:2880092 for all popluations. Skipping.
[2023-06-25 10:11:35 - INFO] Preparing data at region 1:2880092-1:5001596. Skipping if following warning occurs.
[2023-06-25 10:11:35 - INFO] Deciding prior probability for a gene to be causal.
[2023-06-25 10:11:35 - INFO] Using gencode file prior probability 0.029411764705882353.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:2880092-1:5001596 at EA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:2880092-1:5001596 at AA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:2880092-1:5001596 for all popluations. Skipping.
[2023-06-25 10:11:35 - INFO] Preparing data at region 1:5001596-1:7246891. Skipping if following warning occurs.
[2023-06-25 10:11:35 - INFO] Deciding prior probability for a gene to be causal.
[2023-06-25 10:11:35 - INFO] Using gencode file prior probability 0.02631578947368421.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:5001596-1:7246891 at EA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:5001596-1:7246891 at AA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:35 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:5001596-1:7246891 for all popluations. Skipping.
[2023-06-25 10:11:35 - INFO] Preparing data at region 1:7246891-1:9472400. Skipping if following warning occurs.
[2023-06-25 10:11:35 - INFO] Deciding prior probability for a gene to be causal.
[2023-06-25 10:11:35 - INFO] Using gencode file prior probability 0.018518518518518517.
[2023-06-25 10:11:35 - INFO] No GWAS SNPs with p-value < 5e-08 found at region 1:7246891-1:9472400 at AA_WBC_new_munged_chr1.tsv.
[2023-06-25 10:11:42 - ERROR] fine_map() missing 1 required positional argument: 'prior_chisq'
[2023-06-25 10:11:42 - INFO] Finished TWAS & fine-mapping. Thanks for using FOCUS, and have a nice day!
It would be appreciated a lot for your help with the error. Looking forward to your reply. Thanks a lot.
Can you check that ma-focus is installed? It looks like you are calling it manually. What happens if you load python, and typing
import pyfocus
print(pyfocus.__version__)@quattro prof. Mancuso, thanks so much for your reply. It seems that we exactly did not get the ma-focus installed. We reinstalled it and now we can run the code. Thank you for your time and efforts again.
No worries! Glad it all worked out.