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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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Starting up MAGpy #47

Open naturepoker opened 2 years ago

naturepoker commented 2 years ago

I'm sure this is an issue with me having never used snakemake before, but here goes:

I followed the steps on the github readme (test and building diamond database all worked perfectly), and am now trying to start the actual MAGpy process using the command:

snakemake -rp -s MAGpy --use-conda MAGpy --cores 8

My MAGs are in the mags directory in the cloned github repo.

The process fails with below message:

Building DAG of jobs... MissingRuleException: No rule to produce MAGpy (if you use input functions make sure that they don't raise unexpected exceptions).

Could you point me in the right direction? Thank you!

gaworj commented 1 year ago

Hi, I have encountered exactly the same problem and don't know how to solve it.

Bests, Jan

PeterCx commented 1 year ago

I am having the exact same issue also. Did anyone find a workaround for this? Many thanks

Kind regards,

P

mw55309 commented 1 year ago

Hi

Sorry for the delay

I think the command should be

snakemake -rp -s MAGpy --use-conda --cores 8

Mick

PeterCx commented 1 year ago

Hi Mick,

By running this command does MAGpy do everything. i.e run CheckM for quality control, build the phylogenetic tree etc etc all in one command? Many thanks

Kind regards,

P

mw55309 commented 1 year ago

Yes, that should run everything - if you have the databases installed first (see README)

PeterCx commented 1 year ago

This is working perfect. Thanks very much