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jean997 / cause

R package for CAUSE
https://jean997.github.io/cause/
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Error: Not all `variants` are in data. #24

Closed bbb801 closed 2 years ago

bbb801 commented 2 years ago

image Hi, When I run your pipeline, I got the error' Not all variants are in data.' Any suggestion? By the way, is it workable to use your pipeline to run on my own summary data? Thank you!

######################################################### Warning message: One or more parsing issues, see problems() for details Error: Not all variants are in data. Execution halted [Wed Dec 1 00:54:56 2021] Error in rule cause: jobid: 61 output: results/tagc_asthmaglg_ldl_cause_1_100.RDS shell: Rscript R/cause.R data/tagc_asthmaglg_ldl_data.RDS data/snps_tagc_asthmaglg_ldl.plink.pruned.txt results/tagc_asthma__glg_ldl_params.RDS 1 100 1 results/tagc_asthmaglg_ldl_cause_1_100.RDS 100 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

jean997 commented 2 years ago

Thanks, I think I found the error. If you re-run cause_setup_pipeline() it should download the fixed version. Alternatively, you can just replace the file R/ld_prune_plink.R with https://github.com/jean997/cause/blob/master/pipeline_code/R/ld_prune_plink.R.

bbb801 commented 2 years ago

Thank you! It is workable. It seems there is a warning of the conflict about the 'dplyr' package. May I know if I could use my own datasets and how to cite this pipeline?

jean997 commented 2 years ago

Yes feel free to use and modify the pipeline as you see fit. Thanks for citing it. If you update it in a way you think would be useful to others feel free to submit a pull request.