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konumat / Trans-Phar

GWAS-TWAS (Transcriptome-wide association study)-Pharmacological library integration pipeline
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ERROR : Parsing GWAS failed for population at #2

Open Truman11Zeng opened 2 years ago

Truman11Zeng commented 2 years ago

I had problem with Trans-Phar while I was running focus, and it looks like this:

         FOCUS v0.802

=================================== focus finemap ../Output/agnu_meta_Output_clean.trans_phar/ ../1000G_EUR_Phase3_plink/1000G.EUR.QC.5 GTEx_Adipose_Subcutaneous.db --chr 5 --tissue Adipose_Subcutaneous --p-threshold 1 --out ../Output/agnu_meta_Output_clean.trans_phar/TWASresults/GTEx_Adipose_Subcutaneous/GTEx_Adipose_Subcutaneous.chr5

Starting log... [2022-08-30 19:17:53 - INFO] Preparing GWAS summary file [2022-08-30 19:17:53 - ERROR] Parsing GWAS failed for population at ../Output/agnu_meta_Output_clean.trans_phar/.[Errno 21] Is a directory: '../Output/agnu_meta_Output_clean.trans_phar/' [2022-08-30 19:17:53 - INFO] Finished twas & fine-mapping

konumat commented 1 year ago

Hi Truman11Zeng. Thank you for your question. Replacing "../Output/agnu_meta_Output_clean.trans_phar/" with "../Output/agnu_meta_Output_clean.trans_phar/[your .gz GWAS summary file]" will work fine. Thank you.

Truman11Zeng commented 1 year ago

Thanks for your patients, I have already solved this problem following your instrution. Thanks a lot!