You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi Alvaro,
I have an error when I followed the tutorial of SPrediXcan. It seems that the GWAS file I prepared is the same as the example.
I wonder why the SNP column name can not find. Thank you very much .
Best wishes,
Crane King
PS:
The head of the GWAS file:
SNP CHR BP A1 A2 Z N FRQ beta se z pval
rs11250701 10 1689546 A G 0.514064827551 10480.9119402 0.3588 0.00986809128193 0.0115398329315 0.855132941739 0.392477554721
rs3750679 10 1228623 T C 0.286823567907 11272.3267685 0.3181 0.003938126234 0.0115548679411 0.340819666142 0.733239344476
rs1079389 10 1161980 A G -1.33442191526 12795.4215107 0.0616 -0.0158727319187 0.0213125995792 -0.74475813519 0.456417947609
rs904962 10 1372501 T C 0.388541499779 9608.96696345 0.0726 0.00469197622864 0.0220624100173 0.21266834516 0.831585658841
The error:
./SPrediXcan.py \
--model_db_path /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/PsychENCODE_brain_prefrontal_cortex.db
--covariance /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/covariance.PsychENCODE.txt.gz
--gwas_folder /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data
--gwas_file_pattern ".*gz"
--snp_column SNP
--effect_allele_column A1
--non_effect_allele_column A2
--beta_column beta
--pvalue_column pval
--output_file /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/result/test.csv
INFO - Processing GWAS command line parameters
INFO - Building beta for BIP_mtag.txt.gz and /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/PsychENCODE_brain_prefrontal_cortex.db
INFO - Reading input gwas with special handling: /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/BIP_mtag.txt.gz
INFO - Processing input gwas
INFO - Aligning GWAS to models
INFO - Trimming output
INFO - Building beta for PsychENCODE.txt.gz and /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/PsychENCODE_brain_prefrontal_cortex.db
INFO - Reading input gwas with special handling: /media/EXTend2018/Wanghe2019/traits/TwosampleMR/JTI/MetaXcan/data/PsychENCODE.txt.gz
ERROR - Did not find snp colum name
The text was updated successfully, but these errors were encountered:
Hi Alvaro,
I have an error when I followed the tutorial of SPrediXcan. It seems that the GWAS file I prepared is the same as the example.
I wonder why the SNP column name can not find. Thank you very much .
Best wishes,
Crane King
PS:
The head of the GWAS file:
SNP CHR BP A1 A2 Z N FRQ beta se z pval
rs11250701 10 1689546 A G 0.514064827551 10480.9119402 0.3588 0.00986809128193 0.0115398329315 0.855132941739 0.392477554721
rs3750679 10 1228623 T C 0.286823567907 11272.3267685 0.3181 0.003938126234 0.0115548679411 0.340819666142 0.733239344476
rs1079389 10 1161980 A G -1.33442191526 12795.4215107 0.0616 -0.0158727319187 0.0213125995792 -0.74475813519 0.456417947609
rs904962 10 1372501 T C 0.388541499779 9608.96696345 0.0726 0.00469197622864 0.0220624100173 0.21266834516 0.831585658841
The error:
./SPrediXcan.py \
The text was updated successfully, but these errors were encountered: