I’m trying to run a workflow on snakemake. I have to automate a couple of steps which are depending all on python scripts or pipelines already made. My rule Gene_flow_between _species has to run once on each list of genomes and build a core-genome as output for each run (for a total of three runs). Snakemake seems to be able to locate the input files and to start to complete the first steps of the first run in the workflow, but for some reason exits out with MissingOutput Exception error stating it cannot find the output files for the second and the third runs of the workflow.

I’m trying to run a workflow on snakemake. I have to automate a couple of steps which are depending all on python scripts or pipelines already made. My rule Gene_flow_between _species has to run once on each list of genomes and build a core-genome as output for each run (for a total of three runs). Snakemake seems to be able to locate the input files and to start to complete the first steps of the first run in the workflow, but for some reason exits out with MissingOutput Exception error stating it cannot find the output files for the second and the third runs of the workflow.