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konumat / Trans-Phar

GWAS-TWAS (Transcriptome-wide association study)-Pharmacological library integration pipeline
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Error: fine_map() got an unexpected keyword argument 'prior_chisq' #4

Open henkt7 opened 1 year ago

henkt7 commented 1 year ago

Hi, I'm running into an error related to the prior_chisq argument for fine_map(). Just installed, working with python 3.7.3. Any suggestions would be welcome!

      FOCUS v0.802

=================================== focus finemap ../Output/Schizo/Schizo_munge.sumstats.gz ../1000G_EUR_Phase3_plink/1000G.EUR.QC.1 GTEx_Adipose_Subcutaneous.db --chr 1 --tissue Adipose_Subcutaneous --p-threshold 1 --locations /projects/transphar/Trans-Phar/focus/pyfocus/data/ld_blocks/grch37.eur.loci.bed --out ../Output/Schizo/TWASresults/GTEx_Adipose_Subcutaneous/GTEx_Adipose_Subcutaneous.chr1

Starting log... [2023-05-29 18:00:53 - INFO] Preparing GWAS summary file [2023-05-29 18:01:23 - INFO] Preparing reference SNP data [2023-05-29 18:01:25 - INFO] Preparing weight database [2023-05-29 18:01:25 - INFO] Preparing user-defined locations [2023-05-29 18:01:25 - INFO] Prioritizing genes by Adipose_Subcutaneous tissue then on predictive performance at region 1:13110 - 1:1892325 [2023-05-29 18:01:25 - ERROR] fine_map() got an unexpected keyword argument 'prior_chisq' [2023-05-29 18:01:25 - INFO] Finished twas & fine-mapping

henkt7 commented 1 year ago

Update: as a test I ran focus outside of the Trans-Phar pipeline using the already cleaned tutorial Schizophrenia sumstats and the focus.db weight database (from https://github.com/bogdanlab/focus/wiki) and didn't run into the above error then. So, might be Trans-Phar pipeline where error arises?

focus finemap ../../Output/Schizo/Schizo_munge.sumstats.gz ../../1000G_EUR_Phase3_plink/1000G.EUR.QC.22 ../focus.db --chr 22 --locations /projects/transphar/Trans-Phar/focus/pyfocus/data/ld_blocks/grch37.eur.loci.bed --tissue adipose --out ../test_output/test_ch22

1667857557 commented 1 year ago

Update: as a test I ran focus outside of the Trans-Phar pipeline using the already cleaned tutorial Schizophrenia sumstats and the focus.db weight database (from https://github.com/bogdanlab/focus/wiki) and didn't run into the above error then. So, might be Trans-Phar pipeline where error arises?

focus finemap ../../Output/Schizo/Schizo_munge.sumstats.gz ../../1000G_EUR_Phase3_plink/1000G.EUR.QC.22 ../focus.db --chr 22 --locations /projects/transphar/Trans-Phar/focus/pyfocus/data/ld_blocks/grch37.eur.loci.bed --tissue adipose --out ../test_output/test_ch22

We have encountered the same error. Have you found a solution to the problem？

shinichinamba commented 11 months ago

It appears that the issue is not stemming from Trans-Phar itself but rather from the recent upgrade of FOCUS. The FOCUS group has recently established a new GitHub page and released the latest version, which unfortunately is not compatible with the previous version. Trans-Phar specifies an older version of FOCUS, so attempting to run Trans-Phar in an environment with a newer version of FOCUS installed will result in an error. To mitigate this, we recommend creating a separate environment for Trans-Phar using pyenv or other environment-management tools.

1667857557 commented 11 months ago

Thanks a lot!

It appears that the issue is not stemming from Trans-Phar itself but rather from the recent upgrade of FOCUS. The FOCUS group has recently established a new GitHub page and released the latest version, which unfortunately is not compatible with the previous version. Trans-Phar specifies an older version of FOCUS, so attempting to run Trans-Phar in an environment with a newer version of FOCUS installed will result in an error. To mitigate this, we recommend creating a separate environment for Trans-Phar using pyenv or other environment-management tools.