Thank you so much for developing this great tool! It makes our research easier! I have tried to run it recently, however, it gave me this error message: Error: Duplicate ID 's00007:1500001' generated by --set-missing-var-ids. It stopped when trying to convert vcf to plink bed file: subprocess.CalledProcessError: Command '['plink', '--vcf', '_vcf2gwas_temp_20230408_143339/mod_sub_Flupicolide_sensitivity.part1_snaps_all_v3.vcf.gz', '--make-bed', '--out', '_vcf2gwas_temp_20230408_143339/mod_sub_Flupicolide_sensitivity.part1_snaps_all_v3', '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', '64000', '--threads', '16']' returned non-zero exit status 5.
Would you happen to have any recommendations for me to fix this bug? Appreciate your support!
The issue should be fixed now in vcf2gwas v0.8.9. Internally I changed the pipeline to use plink2 instead of plink1 for creating the bed files, which has better handling of duplicate IDs generated by missing IDs.
Hi,
Thank you so much for developing this great tool! It makes our research easier! I have tried to run it recently, however, it gave me this error message: Error: Duplicate ID 's00007:1500001' generated by --set-missing-var-ids. It stopped when trying to convert vcf to plink bed file: subprocess.CalledProcessError: Command '['plink', '--vcf', '_vcf2gwas_temp_20230408_143339/mod_sub_Flupicolide_sensitivity.part1_snaps_all_v3.vcf.gz', '--make-bed', '--out', '_vcf2gwas_temp_20230408_143339/mod_sub_Flupicolide_sensitivity.part1_snaps_all_v3', '--mind', '1', '--set-missing-var-ids', '@:#', '--allow-extra-chr', '--memory', '64000', '--threads', '16']' returned non-zero exit status 5.
Would you happen to have any recommendations for me to fix this bug? Appreciate your support!
Thanks,
Li