Rule Exception in rule bam2gvcf - Attribute error

harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

MIT License

63 stars 30 forks source link

Rule Exception in rule bam2gvcf - Attribute error #187

Closed spilornis-ng closed 1 month ago

spilornis-ng commented 1 month ago

Hi! I am getting the above error while running the workflow. I checked the config.yaml in default profile and can't really pin-point the issue. Any help will be great!

Thanks!

cademirch commented 1 month ago

What was your command line? You need to make sure to have the --profile specified

spilornis-ng commented 1 month ago

snakemake -s ./snpArcher/workflow/Snakefile -d ./IBB_trial/ --cores 48 --conda-frontend conda --use-conda

Used this as the command line. I thought that by default it uses Default profile, so didn't specify it particularly. Will try running it with --profile flag.

spilornis-ng commented 1 month ago

This worked. Thanks! I am closing this now.