Hi @jlhudd, I have a bit of a follow up to this (or maybe a separate issue with a similar error message).
I think I am encountering a somewhat related error, though I’ve made some major changes to the pipeline by using a totally custom subsampling scheme that has replaced the entirety of the standard workflow up to the
augur tree step, so hopefully this is still a relevant question.
I have some builds that are also getting the
Missing input files for rule all error. These builds are all defined in the
builds.yaml file (sorry for using screenshots instead of direct blockquotes, there is a lot of less important cruft from other builds that I’m omitting, and I was having trouble formatting my indentations ):
Oddly I get errors for the build titled
P.1 (and for the other Pango-based builds that are collapsed), but not for the
demo build at the top.
I have confirmed that my
Snakefile) rule’s input:
matches the output of the last rule from my workflow (in
When I try to run things I get the input file error:
$ time snakemake --cores 35 --profile my_profiles/sars-cov-2-belgium/ -p
Building DAG of jobs…
MissingInputException in line 75 of ~/projects/sars-cov-2-belgium/Snakefile:
Missing input files for rule all:
I should also note that the builds shown in the
builds.yaml file that don’t appear as errors here are the ones that already have their
json files in the
auspice directory, as they were completed under a previous version of the pipeline.
My only guesses at this time are that either I broke a connection between
main_workflow.smk somehow, or that something with how I’ve formatted my
builds.yaml file is wrong.