Hi when I run the run_coloc.py for the example data
python3.7 $REPO/run_coloc.py -gwas_mode pvalue -gwas $DATA/processed_summary_imputation/imputed_CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz -eqtl_mode bse -eqtl GTEx_Analysis_v8_eQTL/Whole-Blood.v8.signif-variant-gene-pairs.txt.gz -gwas_sample_size 149461 -eqtl_sample_size 670 -p1 2.4769e-05 -p2 0.00288782 -p12 1.264e-06 -parsimony 8 -output CARDIoGRAM_C4D_CAD_ADDITIVE_Whole_Blood.txt.gz
I got this error:
File "/scg/apps/software/summary-gwas-imputation/20220620/bin/run_coloc.py", line 67, in
run(args)
File "/apps/software/summary-gwas-imputation/20220620/bin/run_coloc.py", line 12, in run
Coloc.initialize(args.coloc_script)
File "/apps/software/summary-gwas-imputation/20220620/bin/genomic_tools_lib/external_tools/coloc/Coloc.py", line 25, in initialize
coloc_r = importr('coloc').coloc_abf
File "/home/.conda/envs/Coloc/lib/python3.7/site-packages/rpy2/robjects/packages.py", line 453, in importr
env = _get_namespace(rname)
Hi when I run the run_coloc.py for the example data python3.7 $REPO/run_coloc.py -gwas_mode pvalue -gwas $DATA/processed_summary_imputation/imputed_CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz -eqtl_mode bse -eqtl GTEx_Analysis_v8_eQTL/Whole-Blood.v8.signif-variant-gene-pairs.txt.gz -gwas_sample_size 149461 -eqtl_sample_size 670 -p1 2.4769e-05 -p2 0.00288782 -p12 1.264e-06 -parsimony 8 -output CARDIoGRAM_C4D_CAD_ADDITIVE_Whole_Blood.txt.gz
I got this error: File "/scg/apps/software/summary-gwas-imputation/20220620/bin/run_coloc.py", line 67, in
run(args)
File "/apps/software/summary-gwas-imputation/20220620/bin/run_coloc.py", line 12, in run
Coloc.initialize(args.coloc_script)
File "/apps/software/summary-gwas-imputation/20220620/bin/genomic_tools_lib/external_tools/coloc/Coloc.py", line 25, in initialize
coloc_r = importr('coloc').coloc_abf
File "/home/.conda/envs/Coloc/lib/python3.7/site-packages/rpy2/robjects/packages.py", line 453, in importr
env = _get_namespace(rname)
Do you know what is wrong?