Missing rule

[mlcossette9224]

Hi,

I want to use your pipeline to find gene duplication in other mammals and am running into some issues while testing it out.

I am trying to run the first step: "Generate the modified hg38 for reciprocal best hit searches using your query file of interest:
snakemake --use-conda output/recBlastDBPrep/hg38_maskRep_noVarChr_fragWithGenes.2bit"

and am getting the following error:

"localrules directive specifies rules that are not present in the Snakefile:
all

Building DAG of jobs...
MissingRuleException:
No rule to produce output/recBlastDBPrep/hg38_maskRep_noVarChr_fragWithGenes.2bit (if you use input functions make sure that they don't raise unexpected exceptions)."

I have looked in all the directories and files and cannot find this rule. Would it be possible to get the updated file to make this work? Or how has the genome been modified to make the pipeline run? Other commands seem to work so far but this is the only one that is not working.
Thanks,

Marie