Running metaGEM with preprocessed data

[AryLech]

Hello,

I'd like to use your tool, specifically the following modules:

Reconstruct & evaluate genome-scale metabolic models with CarveMe and memote

Species metabolic coupling analysis with SMETANA

For this, I plan to use previously processed data (i.e., reads have already been filtered, assembled, binned, and taxonomically and functionally annotated).

Is it possible to start directly from that point?

I've tried running the following command:

bash metaGEM.sh -t createFolders -l

But I got the following error:

Building DAG of jobs...
MissingInputException in line 34 of /home/arely/metaGEM/workflow/Snakefile:
Missing input files for rule createFolders:
/path/to/project/folder/on/your/cluster

Then I tried:
bash metaGEM.sh -t carveme -j 4 -c 16 -m 120 -l -h 2

(In this case, I used annotated protein sequences in FASTA format placed in a folder named proteinBins.)

The command executed as a dry run and seemed to complete without errors, but I’m not sure if that’s the correct way to start with my custom input.

Job counts:
	count	jobs
	1	all
	1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
Do you wish to submit this batch of jobs on your local machine? (y/n)y   
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job counts:
	count	jobs
	1	all
	1
Select jobs to execute...
Gathering  ... 
[Thu May  8 00:20:29 2025]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/arely/metaGEM/workflow/.snakemake/log/2025-05-08T002029.873643.snakemake.log

I also ran:
bash metaGEM.sh -t check
And got the following:

CondaError: Run 'conda init' before 'conda activate'
...
Some folders appear to be missing, do you wish to run the createFolders Snakefile rule? (y/n)y
...
MissingInputException in line 34...
There are no sequencing files (*.gz) in the dataset folder!
Please download or move your paired end files into sample specific subfolders within the dataset folder.
]

I do not plan to use raw sequencing data

Could you please confirm if it's possible to run only the CarveMe and SMETANA modules with processed inputs, and if so, how should I properly configure the folder structure and config.yaml?

Thank you very much!