ERROR] pivot() takes 1 positional argument but 4 were given

[Truman11Zeng]

while running Focus Finemap, I encountered some issues,the running log lists as following, could you please show me how to solve it, thank you!

         FOCUS v0.802

===================================
focus finemap
/mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz
/mnt/sdb/prog/Trans-Phar/1000G_EUR_Phase3_plink/1000G.EUR.QC.22
/mnt/sdb/prog/Trans-Phar/db/GTEx_Whole_Blood.db
--chr 22
--tissue GTEx_Whole_Blood
--locations 37:EUR
--out NAFLD3metal_GTEx_Whole_Blood_22

Starting log...
[2024-05-11 00:37:11 - INFO] Detecting 1 populations for fine-mapping.
[2024-05-11 00:37:11 - INFO] As a result, running single-population FOCUS.
[2024-05-11 00:37:11 - INFO] Preparing GWAS summary file for population at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz.
[2024-05-11 00:37:11 - INFO] Preparing reference SNP data for population at /mnt/sdb/prog/Trans-Phar/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.
[2024-05-11 00:37:11 - INFO] Preparing weight database at /mnt/sdb/prog/Trans-Phar/db/GTEx_Whole_Blood.db.
[2024-05-11 00:37:11 - INFO] Preparing user-defined locations at 37:EUR.
[2024-05-11 00:37:11 - INFO] Found 1703 independent regions on the entire genome.
[2024-05-11 00:37:11 - INFO] 24 independent regions currently used after being filtered on chromosome, start, and stop.
[2024-05-11 00:37:11 - INFO] Preparing data at region 22:16050408-22:17674295. Skipping if following warning occurs.
[2024-05-11 00:37:11 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:11 - INFO] Using gencode file prior probability 0.016666666666666666.
[2024-05-11 00:37:11 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:16050408-22:17674295 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:11 - INFO] Preparing data at region 22:17674295-22:18296088. Skipping if following warning occurs.
[2024-05-11 00:37:11 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:11 - INFO] Using gencode file prior probability 0.058823529411764705.
[2024-05-11 00:37:11 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:17674295-22:18296088 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:11 - INFO] Preparing data at region 22:18296088-22:19912358. Skipping if following warning occurs.
[2024-05-11 00:37:11 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:11 - INFO] Using gencode file prior probability 0.013513513513513514.
[2024-05-11 00:37:11 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:18296088-22:19912358 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:11 - INFO] Preparing data at region 22:19912358-22:22357325. Skipping if following warning occurs.
[2024-05-11 00:37:11 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:11 - INFO] Using gencode file prior probability 0.006666666666666667.
[2024-05-11 00:37:11 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:19912358-22:22357325 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:11 - INFO] Preparing data at region 22:22357325-22:23712647. Skipping if following warning occurs.
[2024-05-11 00:37:11 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.008620689655172414.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:22357325-22:23712647 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:23712647-22:24984204. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.016666666666666666.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:23712647-22:24984204 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:24984204-22:26791628. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.018867924528301886.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:24984204-22:26791628 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:26791628-22:27834752. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.045454545454545456.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:26791628-22:27834752 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:27834752-22:29651799. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.023255813953488372.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:27834752-22:29651799 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:29651799-22:31439918. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.013888888888888888.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:29651799-22:31439918 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:31439918-22:32664986. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.02040816326530612.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:31439918-22:32664986 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:32664986-22:34494914. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:12 - INFO] Using gencode file prior probability 0.0625.
[2024-05-11 00:37:12 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:32664986-22:34494914 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:12 - INFO] Preparing data at region 22:34494914-22:35530985. Skipping if following warning occurs.
[2024-05-11 00:37:12 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.047619047619047616.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:34494914-22:35530985 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:35530985-22:37570269. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.014925373134328358.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:35530985-22:37570269 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:37570269-22:39307894. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.01282051282051282.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:37570269-22:39307894 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:39307894-22:40545797. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.03333333333333333.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:39307894-22:40545797 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:40545797-22:42690818. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.011363636363636364.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:40545797-22:42690818 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:42690818-22:43714200. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.043478260869565216.
[2024-05-11 00:37:13 - WARNING] No GWAS SNPs with p-value < 5e-08 found at region 22:42690818-22:43714200 at /mnt/sdb/prog/Trans-Phar/Output/NAFLDmetal.trans-phar/NAFLDmetal.trans-phar_munge.chr22.sumstats.gz. Skipping.
[2024-05-11 00:37:13 - INFO] Preparing data at region 22:43714200-22:44995308. Skipping if following warning occurs.
[2024-05-11 00:37:13 - INFO] Deciding prior probability for a gene to be causal.
[2024-05-11 00:37:13 - INFO] Using gencode file prior probability 0.03333333333333333.
[2024-05-11 00:37:14 - INFO] Prioritizing genes by GTEx_Whole_Blood tissue then on predictive performance at region 22:43714255 - 22:44995097 of /mnt/sdb/prog/Trans-Phar/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.
[2024-05-11 00:37:14 - INFO] Fine-mapping starts at region 22:43714200-22:44995308.
[2024-05-11 00:37:14 - INFO] Aligning GWAS, LD, and eQTL weights for the single population. Region 22:43714200-22:44995308 will skip if following errors occur.
[2024-05-11 00:37:14 - INFO] Find 3 common genes to be fine-mapped at region 22:43714200-22:44995308.
[2024-05-11 00:37:14 - INFO] Running TWAS for the single population.
[2024-05-11 00:37:14 - INFO] Calculating PIPs.
[2024-05-11 00:37:14 - ERROR] pivot() takes 1 positional argument but 4 were given
[2024-05-11 00:37:14 - INFO] Finished TWAS & fine-mapping. Thanks for using FOCUS, and have a nice day!