ERROR: __init__() got multiple values for argument 'schema'

[Pierre9344]

Hello,

I installed focus yesterday and try to realize a finemapping analysis but I got the error next:

$ focus finemap ./GWASsum/SCZ_focus.sumstats ./LDref_1 focus.db --chr 1 --tissue blood --out finemap_SCZ.chr1 --locations 37:EUR
===================================
             FOCUS v0.803
===================================
focus finemap
        ./GWASsum/SCZ_focus.sumstats
        ./LDref_1
        focus.db
        --chr 1
        --tissue blood
        --out finemap_SCZ.chr1
        --locations 37:EUR

Starting log...
[2023-09-14 08:23:18 - INFO] Detecting 1 populations for fine-mapping.
[2023-09-14 08:23:18 - INFO] As a result, running single-population FOCUS.
[2023-09-14 08:23:18 - INFO] Preparing GWAS summary file for population at ./GWASsum/SCZ_focus.sumstats.
[2023-09-14 08:23:26 - INFO] Preparing reference SNP data for population at ./LDref_1.
[2023-09-14 08:23:28 - INFO] Preparing weight database at focus.db.
[2023-09-14 08:23:28 - INFO] Preparing user-defined locations at 37:EUR.
[2023-09-14 08:23:28 - INFO] Found 1703 independent regions on the entire genome.
[2023-09-14 08:23:28 - INFO] 133 independent regions currently used after being filtered on chromosome, start, and stop.
[2023-09-14 08:23:28 - INFO] Preparing data at region 1:10583-1:1892607. Skipping if following warning occurs.
[2023-09-14 08:23:28 - INFO] Deciding prior probability for a gene to be causal.
[2023-09-14 08:23:28 - INFO] Using gencode file prior probability 0.007575757575757576.
[2023-09-14 08:23:28 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:10583-1:1892607 at ./GWASsum/SCZ_focus.sumstats. Skipping.
[2023-09-14 08:23:28 - INFO] Preparing data at region 1:1892607-1:3582736. Skipping if following warning occurs.
[2023-09-14 08:23:28 - INFO] Deciding prior probability for a gene to be causal.
[2023-09-14 08:23:28 - INFO] Using gencode file prior probability 0.02127659574468085.
[2023-09-14 08:23:28 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:1892607-1:3582736 at ./GWASsum/SCZ_focus.sumstats. Skipping.
[2023-09-14 08:23:28 - INFO] Preparing data at region 1:3582736-1:4380811. Skipping if following warning occurs.
[2023-09-14 08:23:28 - INFO] Deciding prior probability for a gene to be causal.
[2023-09-14 08:23:28 - INFO] Using gencode file prior probability 0.05.
[2023-09-14 08:23:28 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:3582736-1:4380811 at ./GWASsum/SCZ_focus.sumstats. Skipping.
[2023-09-14 08:23:28 - INFO] Preparing data at region 1:4380811-1:5913893. Skipping if following warning occurs.
[2023-09-14 08:23:28 - INFO] Deciding prior probability for a gene to be causal.
[2023-09-14 08:23:29 - INFO] Using gencode file prior probability 0.09090909090909091.
[2023-09-14 08:23:29 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 1:4380811-1:5913893 at ./GWASsum/SCZ_focus.sumstats. Skipping.
[2023-09-14 08:23:29 - INFO] Preparing data at region 1:5913893-1:7247335. Skipping if following warning occurs.
[2023-09-14 08:23:29 - INFO] Deciding prior probability for a gene to be causal.
[2023-09-14 08:23:29 - INFO] Using gencode file prior probability 0.03125.
[2023-09-14 08:23:29 - ERROR] __init__() got multiple values for argument 'schema'
[2023-09-14 08:23:29 - INFO] Finished TWAS & fine-mapping. Thanks for using FOCUS, and have a nice day!

Does someone have any idea on how I can correct this?

[zeyunlu]

hi, has this issue been solved? It would be great if you can add --verbose to the command.