Starting up MAGpy

[naturepoker]

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]

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

Bests,
Jan

[PeterCx]

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

Kind regards,

P

[mw55309]

Hi

Sorry for the delay

I think the command should be

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

Mick

[PeterCx]

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]

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

[PeterCx]

This is working perfect. Thanks very much